Starting phenix.real_space_refine on Fri Feb 6 09:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.map" model { file = "/net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzr_72077/02_2026/9pzr_72077.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 14898 2.51 5 N 4076 2.21 5 O 4518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23598 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 4919 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 16, 'GLN:plan1': 4, 'GLU:plan': 13, 'TRP:plan': 1, 'ASP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 210 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4906 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 24, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 10, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 4978 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 153 Chain: "D" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4980 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "E" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1010 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'CIS': 3, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 606 Unresolved non-hydrogen dihedrals: 202 Planarities with less than four sites: {'UNK:plan-1': 202} Unresolved non-hydrogen planarities: 202 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 950 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'CIS': 2, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 570 Unresolved non-hydrogen dihedrals: 190 Planarities with less than four sites: {'UNK:plan-1': 190} Unresolved non-hydrogen planarities: 190 Chain: "G" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 970 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'CIS': 3, 'TRANS': 190} Chain breaks: 4 Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 194 Planarities with less than four sites: {'UNK:plan-1': 194} Unresolved non-hydrogen planarities: 194 Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 885 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'CIS': 2, 'TRANS': 174} Chain breaks: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 177 Planarities with less than four sites: {'UNK:plan-1': 177} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 5.28, per 1000 atoms: 0.22 Number of scatterers: 23598 At special positions: 0 Unit cell: (197.25, 127.818, 184.626, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4518 8.00 N 4076 7.00 C 14898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " 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 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6376 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 44 sheets defined 38.2% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.755A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.664A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.566A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 185 removed outlier: 4.487A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.552A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.538A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.516A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.913A pdb=" N ALA A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.948A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.662A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.624A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.535A pdb=" N LYS A 708 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.507A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.571A pdb=" N ASN A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.801A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.779A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.670A pdb=" N GLN B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.862A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.653A pdb=" N ARG B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 4.269A pdb=" N GLN B 336 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 337 " --> pdb=" O LEU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 337' Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.670A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.681A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.655A pdb=" N GLN B 671 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.565A pdb=" N ARG B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 4.327A pdb=" N ARG B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.565A pdb=" N ARG B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 784 removed outlier: 4.655A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.903A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.532A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.555A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 188 removed outlier: 4.075A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 255 removed outlier: 4.002A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.611A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.840A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.627A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.555A pdb=" N SER C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.799A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 668 removed outlier: 4.239A pdb=" N ASN C 668 " --> pdb=" O THR C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.500A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.773A pdb=" N GLU C 707 " --> pdb=" O TYR C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.611A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 removed outlier: 3.511A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.642A pdb=" N SER D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.776A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.661A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.697A pdb=" N GLN D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.885A pdb=" N LEU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 308 Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.532A pdb=" N GLY D 498 " --> pdb=" O ASN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 707 removed outlier: 4.218A pdb=" N ARG D 707 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.965A pdb=" N UNK E 160 " --> pdb=" O UNK E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 149 through 155 Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 210 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.174A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.456A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 221 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.423A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 476 removed outlier: 8.180A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 removed outlier: 4.180A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 74 removed outlier: 6.883A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET B 74 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY B 101 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 205 removed outlier: 9.529A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 228 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 256 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 410 Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB3, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB4, first strand: chain 'B' and resid 533 through 536 removed outlier: 6.645A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 65 removed outlier: 6.187A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.416A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 221 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.593A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.474A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AC3, first strand: chain 'D' and resid 68 through 74 removed outlier: 6.909A pdb=" N ILE D 36 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 72 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 38 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N MET D 74 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 40 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 101 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 98 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 199 through 205 removed outlier: 9.360A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 226 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 228 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 230 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 227 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 474 through 479 removed outlier: 3.563A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 409 " --> pdb=" O MET D 507 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AC7, first strand: chain 'D' and resid 529 through 530 removed outlier: 4.079A pdb=" N VAL D 529 " --> pdb=" O TYR D 761 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 533 through 536 removed outlier: 6.657A pdb=" N GLY D 683 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ASP D 731 " --> pdb=" O GLY D 683 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AD1, first strand: chain 'E' and resid 30 through 32 removed outlier: 6.496A pdb=" N UNK E 30 " --> pdb=" O UNK E 139 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N UNK E 56 " --> pdb=" O UNK E 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 149 through 153 removed outlier: 5.199A pdb=" N UNK E 166 " --> pdb=" O UNK E 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N UNK E 212 " --> pdb=" O UNK E 166 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N UNK E 168 " --> pdb=" O UNK E 210 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N UNK E 210 " --> pdb=" O UNK E 168 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N UNK E 170 " --> pdb=" O UNK E 208 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N UNK E 208 " --> pdb=" O UNK E 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK E 172 " --> pdb=" O UNK E 206 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N UNK E 206 " --> pdb=" O UNK E 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 149 through 153 removed outlier: 5.199A pdb=" N UNK E 166 " --> pdb=" O UNK E 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N UNK E 212 " --> pdb=" O UNK E 166 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N UNK E 168 " --> pdb=" O UNK E 210 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N UNK E 210 " --> pdb=" O UNK E 168 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N UNK E 170 " --> pdb=" O UNK E 208 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N UNK E 208 " --> pdb=" O UNK E 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK E 172 " --> pdb=" O UNK E 206 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N UNK E 206 " --> pdb=" O UNK E 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AD5, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AD6, first strand: chain 'F' and resid 30 through 34 removed outlier: 6.399A pdb=" N UNK F 31 " --> pdb=" O UNK F 133 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N UNK F 135 " --> pdb=" O UNK F 31 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N UNK F 33 " --> pdb=" O UNK F 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK F 110 " --> pdb=" O UNK F 132 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N UNK F 63 " --> pdb=" O UNK F 72 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N UNK F 72 " --> pdb=" O UNK F 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 146 removed outlier: 5.660A pdb=" N UNK F 201 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N UNK F 202 " --> pdb=" O UNK F 192 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 182 through 183 removed outlier: 4.194A pdb=" N UNK F 176 " --> pdb=" O UNK F 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AE1, first strand: chain 'G' and resid 30 through 32 removed outlier: 6.496A pdb=" N UNK G 30 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK G 69 " --> pdb=" O UNK G 56 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N UNK G 58 " --> pdb=" O UNK G 67 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK G 67 " --> pdb=" O UNK G 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 149 through 151 removed outlier: 5.198A pdb=" N UNK G 166 " --> pdb=" O UNK G 212 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N UNK G 212 " --> pdb=" O UNK G 166 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N UNK G 168 " --> pdb=" O UNK G 210 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N UNK G 210 " --> pdb=" O UNK G 168 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N UNK G 170 " --> pdb=" O UNK G 208 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N UNK G 208 " --> pdb=" O UNK G 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK G 172 " --> pdb=" O UNK G 206 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N UNK G 206 " --> pdb=" O UNK G 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 149 through 151 removed outlier: 5.198A pdb=" N UNK G 166 " --> pdb=" O UNK G 212 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N UNK G 212 " --> pdb=" O UNK G 166 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N UNK G 168 " --> pdb=" O UNK G 210 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N UNK G 210 " --> pdb=" O UNK G 168 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N UNK G 170 " --> pdb=" O UNK G 208 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N UNK G 208 " --> pdb=" O UNK G 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK G 172 " --> pdb=" O UNK G 206 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N UNK G 206 " --> pdb=" O UNK G 172 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 179 through 183 Processing sheet with id=AE5, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE6, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.398A pdb=" N UNK H 31 " --> pdb=" O UNK H 133 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N UNK H 135 " --> pdb=" O UNK H 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N UNK H 33 " --> pdb=" O UNK H 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK H 110 " --> pdb=" O UNK H 132 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N UNK H 63 " --> pdb=" O UNK H 72 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N UNK H 72 " --> pdb=" O UNK H 63 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 142 through 146 removed outlier: 5.660A pdb=" N UNK H 201 " --> pdb=" O UNK H 166 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N UNK H 202 " --> pdb=" O UNK H 192 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 182 through 183 removed outlier: 4.194A pdb=" N UNK H 176 " --> pdb=" O UNK H 183 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2622 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: 4.95 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7122 1.34 - 1.46: 4402 1.46 - 1.58: 12320 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 24018 Sorted by residual: bond pdb=" N VAL D 430 " pdb=" CA VAL D 430 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" N HIS A 67 " pdb=" CA HIS A 67 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.01e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.339 1.427 -0.087 3.40e-02 8.65e+02 6.60e+00 bond pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.59e+00 bond pdb=" C UNK H 168 " pdb=" N UNK H 169 " ideal model delta sigma weight residual 1.329 1.364 -0.035 1.40e-02 5.10e+03 6.38e+00 ... (remaining 24013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 31888 2.32 - 4.64: 871 4.64 - 6.96: 50 6.96 - 9.28: 19 9.28 - 11.60: 2 Bond angle restraints: 32830 Sorted by residual: angle pdb=" N UNK G 178 " pdb=" CA UNK G 178 " pdb=" CB UNK G 178 " ideal model delta sigma weight residual 110.50 101.50 9.00 1.70e+00 3.46e-01 2.80e+01 angle pdb=" N UNK E 178 " pdb=" CA UNK E 178 " pdb=" CB UNK E 178 " ideal model delta sigma weight residual 110.50 101.57 8.93 1.70e+00 3.46e-01 2.76e+01 angle pdb=" N UNK E 176 " pdb=" CA UNK E 176 " pdb=" CB UNK E 176 " ideal model delta sigma weight residual 110.50 103.43 7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" N UNK G 176 " pdb=" CA UNK G 176 " pdb=" CB UNK G 176 " ideal model delta sigma weight residual 110.50 103.45 7.05 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CA VAL B 430 " pdb=" C VAL B 430 " pdb=" O VAL B 430 " ideal model delta sigma weight residual 121.97 118.16 3.81 9.80e-01 1.04e+00 1.51e+01 ... (remaining 32825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 13814 15.19 - 30.37: 345 30.37 - 45.56: 71 45.56 - 60.74: 2 60.74 - 75.93: 9 Dihedral angle restraints: 14241 sinusoidal: 4450 harmonic: 9791 Sorted by residual: dihedral pdb=" CA UNK H 209 " pdb=" C UNK H 209 " pdb=" N UNK H 210 " pdb=" CA UNK H 210 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA UNK F 209 " pdb=" C UNK F 209 " pdb=" N UNK F 210 " pdb=" CA UNK F 210 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA UNK H 113 " pdb=" C UNK H 113 " pdb=" N UNK H 114 " pdb=" CA UNK H 114 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 14238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2937 0.047 - 0.093: 747 0.093 - 0.140: 232 0.140 - 0.187: 23 0.187 - 0.234: 5 Chirality restraints: 3944 Sorted by residual: chirality pdb=" CB ILE B 755 " pdb=" CA ILE B 755 " pdb=" CG1 ILE B 755 " pdb=" CG2 ILE B 755 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA UNK G 176 " pdb=" N UNK G 176 " pdb=" C UNK G 176 " pdb=" CB UNK G 176 " both_signs ideal model delta sigma weight residual False 2.52 2.75 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE D 755 " pdb=" CA ILE D 755 " pdb=" CG1 ILE D 755 " pdb=" CG2 ILE D 755 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3941 not shown) Planarity restraints: 4283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 104 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO C 104 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 94 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO A 95 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.037 5.00e-02 4.00e+02 ... (remaining 4280 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 22 2.33 - 2.97: 10722 2.97 - 3.61: 32963 3.61 - 4.26: 49550 4.26 - 4.90: 80916 Nonbonded interactions: 174173 Sorted by model distance: nonbonded pdb=" CB UNK E 198 " pdb=" CB UNK F 190 " model vdw 1.687 3.840 nonbonded pdb=" NH2 ARG A 489 " pdb=" O ASN B 193 " model vdw 1.952 3.120 nonbonded pdb=" OD1 ASP D 421 " pdb=" NZ LYS D 454 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP B 421 " pdb=" NZ LYS B 454 " model vdw 2.105 3.120 nonbonded pdb=" O GLN A 48 " pdb=" NH1 ARG A 52 " model vdw 2.145 3.120 ... (remaining 174168 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 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 58 or (resid 59 and (name N or na \ me CA or name C or name O or name CB )) or resid 60 through 238 or (resid 239 an \ d (name N or name CA or name C or name O or name CB )) or resid 240 through 254 \ or (resid 255 and (name N or name CA or name C or name O or name CB )) or (resid \ 256 through 262 and (name N or name CA or name C or name O or name CB )) or res \ id 263 through 275 or (resid 276 and (name N or name CA or name C or name O or n \ ame CB )) or resid 277 through 296 or (resid 297 through 300 and (name N or name \ CA or name C or name O or name CB )) or resid 301 through 347 or (resid 348 thr \ ough 349 and (name N or name CA or name C or name O or name CB )) or resid 350 t \ hrough 353 or (resid 354 and (name N or name CA or name C or name O or name CB ) \ ) or resid 355 through 360 or (resid 361 through 363 and (name N or name CA or n \ ame C or name O or name CB )) or resid 364 through 496 or (resid 497 and (name N \ or name CA or name C or name O or name CB )) or resid 498 through 676 or (resid \ 677 through 678 and (name N or name CA or name C or name O or name CB )) or res \ id 679 through 721 or (resid 722 and (name N or name CA or name C or name O or n \ ame CB )) or resid 723 through 789 or (resid 790 and (name N or name CA or name \ C or name O or name CB )) or resid 791 through 793 or (resid 794 and (name N or \ name CA or name C or name O or name CB )) or resid 795 through 797)) selection = (chain 'C' and (resid 25 through 35 or (resid 36 through 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 39 or (resid 40 through \ 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (res \ id 43 through 45 and (name N or name CA or name C or name O or name CB )) or res \ id 46 through 47 or (resid 48 through 49 and (name N or name CA or name C or nam \ e O or name CB )) or resid 50 through 71 or (resid 72 and (name N or name CA or \ name C or name O or name CB )) or resid 73 through 99 or (resid 100 through 102 \ and (name N or name CA or name C or name O or name CB )) or resid 103 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 173 or (resid 174 through 176 and (name N or name CA or name C or \ name O or name CB )) or resid 177 or (resid 178 and (name N or name CA or name C \ or name O or name CB )) or resid 179 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 through 209 or (resid 210 \ through 211 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 2 or (resid 213 and (name N or name CA or name C or name O or name CB )) or resi \ d 214 through 224 or (resid 225 and (name N or name CA or name C or name O or na \ me CB )) or resid 226 through 250 or (resid 251 and (name N or name CA or name C \ or name O or name CB )) or resid 252 through 312 or (resid 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 315 or (resid 316 \ and (name N or name CA or name C or name O or name CB )) or resid 317 through 32 \ 1 or (resid 322 through 323 and (name N or name CA or name C or name O or name C \ B )) or resid 324 through 336 or (resid 337 and (name N or name CA or name C or \ name O or name CB )) or resid 338 or (resid 339 and (name N or name CA or name C \ or name O or name CB )) or resid 340 through 341 or (resid 342 and (name N or n \ ame CA or name C or name O or name CB )) or resid 343 through 375 or (resid 376 \ through 378 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 9 through 416 or (resid 417 and (name N or name CA or name C or name O or name C \ B )) or resid 418 through 420 or (resid 421 and (name N or name CA or name C or \ name O or name CB )) or resid 422 or (resid 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 through 426 or (resid 427 and (name N or n \ ame CA or name C or name O or name CB )) or resid 428 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 69 \ 4 or (resid 695 and (name N or name CA or name C or name O or name CB )) or resi \ d 696 through 697 or (resid 698 and (name N or name CA or name C or name O or na \ me CB )) or resid 699 through 797)) } ncs_group { reference = (chain 'B' and (resid 34 through 201 or (resid 202 and (name N or name CA or nam \ e C or name O or name CB )) or resid 203 through 213 or (resid 214 and (name N o \ r name CA or name C or name O or name CB )) or resid 215 through 391 or (resid 3 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 393 through \ 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) or r \ esid 399 through 419 or (resid 420 and (name N or name CA or name C or name O or \ name CB )) or resid 421 through 674 or (resid 675 through 677 and (name N or na \ me CA or name C or name O or name CB )) or resid 678 through 753 or (resid 754 a \ nd (name N or name CA or name C or name O or name CB )) or resid 755 through 780 \ or (resid 781 and (name N or name CA or name C or name O or name CB )) or resid \ 782 through 800)) selection = (chain 'D' and (resid 34 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 54 or (resid 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 180 or (resid 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 90 or (resid 291 and (name N or name CA or name C or name O or name CB )) or res \ id 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or \ resid 294 through 307 or (resid 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 314 or (resid 315 through 316 and (name N or \ name CA or name C or name O or name CB )) or resid 317 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or resid \ 330 through 345 or (resid 346 and (name N or name CA or name C or name O or name \ CB )) or resid 347 through 351 or (resid 352 through 353 and (name N or name CA \ or name C or name O or name CB )) or resid 354 through 380 or (resid 381 and (n \ ame N or name CA or name C or name O or name CB )) or resid 382 through 449 or ( \ resid 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 456 or (resid 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 464 or (resid 465 and (name N or name CA or name C or na \ me O or name CB )) or resid 466 through 723 or (resid 724 and (name N or name CA \ or name C or name O or name CB )) or resid 725 through 800)) } ncs_group { reference = (chain 'E' and resid 46 through 244) selection = (chain 'F' and resid 36 through 244) selection = (chain 'G' and resid 39 through 244) selection = chain 'H' } 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: 1.070 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.080 Find NCS groups from input model: 0.500 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1928 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 : 0.005 0.313 24028 Z= 0.322 Angle : 0.835 11.602 32848 Z= 0.446 Chirality : 0.046 0.234 3944 Planarity : 0.006 0.076 4283 Dihedral : 8.361 75.927 7838 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.10 % Allowed : 1.29 % Favored : 98.62 % 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: -3.86 (0.13), residues: 2579 helix: -2.30 (0.12), residues: 877 sheet: -1.80 (0.25), residues: 401 loop : -3.03 (0.14), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 681 TYR 0.019 0.002 TYR D 180 PHE 0.021 0.002 PHE D 183 TRP 0.020 0.002 TRP A 315 HIS 0.012 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00457 (24018) covalent geometry : angle 0.83511 (32830) SS BOND : bond 0.00091 ( 9) SS BOND : angle 0.84964 ( 18) hydrogen bonds : bond 0.14434 ( 935) hydrogen bonds : angle 7.39785 ( 2622) Misc. bond : bond 0.31303 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.6470 (p90) cc_final: 0.6206 (p90) REVERT: A 353 ILE cc_start: 0.6839 (mt) cc_final: 0.6627 (mp) REVERT: A 354 MET cc_start: -0.2601 (mmm) cc_final: -0.2993 (mtm) REVERT: A 529 PHE cc_start: 0.3446 (m-10) cc_final: 0.3008 (m-80) REVERT: A 778 LYS cc_start: 0.8240 (tptm) cc_final: 0.7948 (tptp) REVERT: B 536 MET cc_start: -0.1908 (tpp) cc_final: -0.2363 (tpp) REVERT: C 35 THR cc_start: 0.7939 (p) cc_final: 0.7713 (p) REVERT: C 42 PHE cc_start: 0.6513 (t80) cc_final: 0.6212 (t80) REVERT: C 512 MET cc_start: 0.3811 (ttm) cc_final: 0.3129 (mmt) REVERT: C 762 MET cc_start: 0.1785 (mmm) cc_final: 0.0409 (ttm) REVERT: D 336 GLN cc_start: 0.7772 (mm110) cc_final: 0.7312 (mp10) REVERT: D 518 ARG cc_start: 0.1137 (mtt180) cc_final: -0.0253 (mtt90) REVERT: D 536 MET cc_start: 0.1962 (tpp) cc_final: 0.1736 (tpp) REVERT: D 705 MET cc_start: -0.5782 (tmm) cc_final: -0.6144 (ptm) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.1797 time to fit residues: 103.1196 Evaluate side-chains 232 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 146 HIS A 273 ASN A 293 HIS A 371 HIS A 449 HIS A 471 ASN A 525 GLN A 780 HIS B 59 GLN B 111 GLN B 218 GLN B 387 HIS B 451 ASN B 709 ASN B 710 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 371 HIS C 449 HIS C 487 GLN D 154 GLN D 216 GLN D 335 HIS D 387 HIS D 451 ASN ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.143908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.127919 restraints weight = 131120.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.130140 restraints weight = 88331.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.130921 restraints weight = 59816.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.131906 restraints weight = 43887.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.132591 restraints weight = 34065.721| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2726 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24028 Z= 0.148 Angle : 0.623 10.663 32848 Z= 0.315 Chirality : 0.041 0.180 3944 Planarity : 0.005 0.065 4283 Dihedral : 4.313 20.000 3494 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.72 % Allowed : 6.49 % Favored : 91.79 % 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: -2.50 (0.15), residues: 2579 helix: -0.66 (0.16), residues: 897 sheet: -1.60 (0.26), residues: 371 loop : -2.45 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 489 TYR 0.020 0.002 TYR A 456 PHE 0.024 0.002 PHE D 210 TRP 0.025 0.002 TRP A 792 HIS 0.007 0.001 HIS D 702 Details of bonding type rmsd covalent geometry : bond 0.00316 (24018) covalent geometry : angle 0.62291 (32830) SS BOND : bond 0.00307 ( 9) SS BOND : angle 0.85085 ( 18) hydrogen bonds : bond 0.02956 ( 935) hydrogen bonds : angle 5.17223 ( 2622) Misc. bond : bond 0.00349 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 TYR cc_start: 0.1119 (OUTLIER) cc_final: -0.0592 (m-10) REVERT: A 501 MET cc_start: 0.3394 (mpp) cc_final: 0.0050 (mtm) REVERT: A 529 PHE cc_start: 0.4030 (m-10) cc_final: 0.3756 (m-80) REVERT: A 696 GLN cc_start: 0.5667 (mt0) cc_final: 0.5306 (mm110) REVERT: A 758 PHE cc_start: 0.4195 (m-10) cc_final: 0.3637 (m-80) REVERT: A 778 LYS cc_start: 0.8467 (tptm) cc_final: 0.8109 (tptp) REVERT: B 200 MET cc_start: 0.1891 (tpp) cc_final: 0.0871 (tpt) REVERT: B 452 VAL cc_start: 0.4790 (t) cc_final: 0.4585 (t) REVERT: B 466 LYS cc_start: 0.5223 (mtpt) cc_final: 0.5006 (mtmt) REVERT: B 491 ASN cc_start: 0.6230 (p0) cc_final: 0.5749 (p0) REVERT: B 507 MET cc_start: 0.2151 (tmm) cc_final: 0.1616 (mpp) REVERT: B 524 PHE cc_start: -0.1130 (m-80) cc_final: -0.1590 (t80) REVERT: B 536 MET cc_start: -0.1488 (tpp) cc_final: -0.1915 (tpp) REVERT: B 705 MET cc_start: 0.3484 (tmm) cc_final: 0.2516 (tpt) REVERT: B 763 ILE cc_start: 0.1943 (mm) cc_final: 0.1733 (mm) REVERT: C 125 MET cc_start: 0.1253 (tpt) cc_final: 0.0656 (tpt) REVERT: C 326 MET cc_start: 0.7494 (tpt) cc_final: 0.7084 (tpt) REVERT: C 762 MET cc_start: 0.0354 (mmm) cc_final: -0.2926 (ptp) REVERT: D 90 MET cc_start: 0.6465 (ppp) cc_final: 0.5660 (tpt) REVERT: D 138 LYS cc_start: -0.1809 (mttp) cc_final: -0.2171 (mttm) REVERT: D 336 GLN cc_start: 0.7016 (mm110) cc_final: 0.6723 (mp10) REVERT: D 450 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.4951 (ppp) REVERT: D 536 MET cc_start: 0.1200 (tpp) cc_final: 0.0987 (tpp) REVERT: D 701 MET cc_start: 0.2736 (tpt) cc_final: 0.1556 (ptm) outliers start: 36 outliers final: 13 residues processed: 282 average time/residue: 0.1601 time to fit residues: 71.3744 Evaluate side-chains 221 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 511 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.0010 chunk 63 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 130 optimal weight: 0.5980 chunk 278 optimal weight: 50.0000 chunk 220 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.128299 restraints weight = 122673.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.129862 restraints weight = 87405.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.130748 restraints weight = 71541.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.131227 restraints weight = 49747.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.131360 restraints weight = 45704.481| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2579 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24028 Z= 0.104 Angle : 0.542 11.528 32848 Z= 0.272 Chirality : 0.039 0.188 3944 Planarity : 0.004 0.064 4283 Dihedral : 3.988 16.540 3494 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.43 % Allowed : 8.40 % Favored : 90.16 % 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: -1.81 (0.16), residues: 2579 helix: 0.03 (0.17), residues: 910 sheet: -1.22 (0.27), residues: 367 loop : -2.14 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 36 TYR 0.023 0.001 TYR C 456 PHE 0.039 0.002 PHE D 210 TRP 0.028 0.002 TRP A 151 HIS 0.003 0.001 HIS D 702 Details of bonding type rmsd covalent geometry : bond 0.00229 (24018) covalent geometry : angle 0.54201 (32830) SS BOND : bond 0.00157 ( 9) SS BOND : angle 0.53809 ( 18) hydrogen bonds : bond 0.02395 ( 935) hydrogen bonds : angle 4.63748 ( 2622) Misc. bond : bond 0.00368 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.7423 (tp) cc_final: 0.7169 (tt) REVERT: A 209 MET cc_start: 0.8227 (mmp) cc_final: 0.7900 (mmp) REVERT: A 696 GLN cc_start: 0.5795 (mt0) cc_final: 0.5400 (mm110) REVERT: A 778 LYS cc_start: 0.8394 (tptm) cc_final: 0.7984 (tptp) REVERT: B 466 LYS cc_start: 0.5111 (mtpt) cc_final: 0.4498 (mtpt) REVERT: B 491 ASN cc_start: 0.6738 (p0) cc_final: 0.6295 (p0) REVERT: B 536 MET cc_start: -0.1517 (tpp) cc_final: -0.1863 (tpp) REVERT: B 705 MET cc_start: 0.2711 (tmm) cc_final: 0.1938 (tpt) REVERT: B 787 GLU cc_start: 0.0804 (OUTLIER) cc_final: 0.0337 (pt0) REVERT: C 33 LEU cc_start: 0.1720 (OUTLIER) cc_final: 0.1255 (tt) REVERT: C 74 MET cc_start: 0.1799 (tmm) cc_final: 0.1357 (ppp) REVERT: C 762 MET cc_start: 0.0706 (mmm) cc_final: -0.1190 (ptp) REVERT: C 785 MET cc_start: 0.7991 (ppp) cc_final: 0.7734 (ppp) REVERT: D 74 MET cc_start: 0.4783 (mpp) cc_final: 0.4312 (mpp) REVERT: D 112 MET cc_start: 0.1155 (mmt) cc_final: -0.0018 (mmm) REVERT: D 138 LYS cc_start: -0.1781 (mttp) cc_final: -0.2251 (mttm) REVERT: D 199 ASP cc_start: 0.7476 (m-30) cc_final: 0.6717 (p0) REVERT: D 450 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.4499 (ppp) REVERT: D 701 MET cc_start: 0.2532 (tpt) cc_final: 0.2223 (ptm) outliers start: 30 outliers final: 13 residues processed: 236 average time/residue: 0.1584 time to fit residues: 59.4417 Evaluate side-chains 204 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 759 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 205 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 267 optimal weight: 40.0000 chunk 154 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 453 GLN ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.119610 restraints weight = 129109.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.120691 restraints weight = 85299.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.121273 restraints weight = 62330.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.122064 restraints weight = 46761.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.122011 restraints weight = 38274.483| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3346 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24028 Z= 0.115 Angle : 0.561 11.030 32848 Z= 0.281 Chirality : 0.040 0.285 3944 Planarity : 0.004 0.059 4283 Dihedral : 3.995 17.272 3494 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.53 % Allowed : 9.03 % Favored : 89.45 % 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: -1.51 (0.16), residues: 2579 helix: 0.36 (0.17), residues: 903 sheet: -0.97 (0.28), residues: 353 loop : -2.04 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 489 TYR 0.025 0.001 TYR C 456 PHE 0.022 0.002 PHE D 210 TRP 0.024 0.001 TRP C 792 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00252 (24018) covalent geometry : angle 0.56036 (32830) SS BOND : bond 0.00265 ( 9) SS BOND : angle 0.86405 ( 18) hydrogen bonds : bond 0.02466 ( 935) hydrogen bonds : angle 4.49793 ( 2622) Misc. bond : bond 0.00354 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.1567 (OUTLIER) cc_final: 0.0075 (m-80) REVERT: A 696 GLN cc_start: 0.6343 (mt0) cc_final: 0.5802 (mm110) REVERT: B 491 ASN cc_start: 0.6141 (p0) cc_final: 0.5716 (p0) REVERT: B 536 MET cc_start: -0.2092 (tpp) cc_final: -0.2554 (tpp) REVERT: C 33 LEU cc_start: 0.2352 (OUTLIER) cc_final: 0.1912 (tt) REVERT: C 125 MET cc_start: 0.1776 (tpt) cc_final: 0.1564 (mtt) REVERT: C 394 MET cc_start: 0.2906 (pmm) cc_final: 0.2400 (pmm) REVERT: C 514 VAL cc_start: 0.6750 (t) cc_final: 0.6452 (t) REVERT: C 762 MET cc_start: 0.2599 (mmm) cc_final: -0.1777 (ptp) REVERT: D 112 MET cc_start: 0.1431 (mmt) cc_final: 0.0561 (mmm) REVERT: D 133 MET cc_start: -0.0147 (ptm) cc_final: -0.0849 (ptm) REVERT: D 450 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6195 (ppp) REVERT: D 701 MET cc_start: 0.2505 (tpt) cc_final: 0.1949 (ptm) outliers start: 32 outliers final: 18 residues processed: 237 average time/residue: 0.1553 time to fit residues: 58.7507 Evaluate side-chains 210 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 95 optimal weight: 0.1980 chunk 193 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 477 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 GLN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.137987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.121964 restraints weight = 136016.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.124081 restraints weight = 86240.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.124592 restraints weight = 58218.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.125457 restraints weight = 43788.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.125629 restraints weight = 36502.455| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3142 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 24028 Z= 0.100 Angle : 0.540 11.558 32848 Z= 0.268 Chirality : 0.039 0.165 3944 Planarity : 0.004 0.061 4283 Dihedral : 3.864 20.369 3494 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.86 % Allowed : 9.79 % Favored : 88.35 % 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: -1.32 (0.16), residues: 2579 helix: 0.59 (0.17), residues: 913 sheet: -0.93 (0.28), residues: 351 loop : -1.99 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 36 TYR 0.015 0.001 TYR D 230 PHE 0.037 0.002 PHE B 272 TRP 0.016 0.001 TRP D 255 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00215 (24018) covalent geometry : angle 0.54042 (32830) SS BOND : bond 0.00104 ( 9) SS BOND : angle 0.53874 ( 18) hydrogen bonds : bond 0.02237 ( 935) hydrogen bonds : angle 4.32807 ( 2622) Misc. bond : bond 0.00337 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.4034 (mmm) cc_final: 0.3815 (mmm) REVERT: A 696 GLN cc_start: 0.6600 (mt0) cc_final: 0.5892 (mm110) REVERT: A 778 LYS cc_start: 0.8476 (tptm) cc_final: 0.7964 (tptp) REVERT: B 90 MET cc_start: -0.2844 (ttt) cc_final: -0.3235 (mtt) REVERT: B 491 ASN cc_start: 0.6176 (p0) cc_final: 0.5913 (p0) REVERT: B 536 MET cc_start: -0.0786 (tpp) cc_final: -0.1023 (tpp) REVERT: B 705 MET cc_start: 0.3110 (tpt) cc_final: 0.2842 (tpp) REVERT: C 33 LEU cc_start: 0.1106 (OUTLIER) cc_final: 0.0642 (tt) REVERT: C 762 MET cc_start: 0.0872 (mmm) cc_final: -0.3197 (ptm) REVERT: C 784 PHE cc_start: 0.6266 (t80) cc_final: 0.5808 (t80) REVERT: D 112 MET cc_start: 0.0613 (mmt) cc_final: 0.0127 (mmm) REVERT: D 133 MET cc_start: -0.0964 (ptm) cc_final: -0.1456 (ptm) REVERT: D 135 MET cc_start: -0.1397 (tmm) cc_final: -0.2209 (mmt) REVERT: D 450 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.4993 (ppp) REVERT: D 701 MET cc_start: 0.2464 (tpt) cc_final: 0.2017 (ptm) outliers start: 39 outliers final: 22 residues processed: 234 average time/residue: 0.1500 time to fit residues: 56.9078 Evaluate side-chains 207 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 284 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 275 optimal weight: 50.0000 chunk 255 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 771 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 477 HIS C 487 GLN D 119 GLN D 154 GLN D 216 GLN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN D 710 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.135289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.113099 restraints weight = 135668.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.112097 restraints weight = 97959.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.113181 restraints weight = 65319.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.113598 restraints weight = 42637.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.113598 restraints weight = 33161.692| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4140 moved from start: 0.8308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24028 Z= 0.201 Angle : 0.811 20.327 32848 Z= 0.413 Chirality : 0.046 0.240 3944 Planarity : 0.006 0.066 4283 Dihedral : 5.290 28.611 3494 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.34 % Allowed : 10.74 % Favored : 86.91 % 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: -2.12 (0.15), residues: 2579 helix: -0.38 (0.16), residues: 901 sheet: -1.34 (0.28), residues: 323 loop : -2.18 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 36 TYR 0.025 0.003 TYR B 737 PHE 0.039 0.004 PHE C 321 TRP 0.056 0.003 TRP D 255 HIS 0.015 0.002 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00444 (24018) covalent geometry : angle 0.81057 (32830) SS BOND : bond 0.00461 ( 9) SS BOND : angle 1.32831 ( 18) hydrogen bonds : bond 0.03989 ( 935) hydrogen bonds : angle 5.41277 ( 2622) Misc. bond : bond 0.00344 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.4080 (mmm) cc_final: 0.3608 (mmm) REVERT: A 407 PRO cc_start: 0.2718 (Cg_endo) cc_final: 0.1198 (Cg_exo) REVERT: A 410 TYR cc_start: 0.1345 (OUTLIER) cc_final: 0.0651 (m-80) REVERT: A 484 PHE cc_start: 0.2237 (OUTLIER) cc_final: 0.0732 (m-80) REVERT: A 506 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5195 (tt) REVERT: A 696 GLN cc_start: 0.6712 (mt0) cc_final: 0.6302 (mm110) REVERT: A 702 MET cc_start: 0.6699 (mmt) cc_final: 0.6229 (mmm) REVERT: A 765 ASP cc_start: 0.5193 (p0) cc_final: 0.4777 (p0) REVERT: B 135 MET cc_start: -0.3041 (OUTLIER) cc_final: -0.3368 (mtt) REVERT: B 230 TYR cc_start: 0.6174 (t80) cc_final: 0.5936 (m-10) REVERT: B 242 GLU cc_start: 0.3481 (tp30) cc_final: 0.3079 (tp30) REVERT: B 306 MET cc_start: 0.1818 (mtm) cc_final: 0.1453 (ptp) REVERT: B 338 MET cc_start: 0.3978 (mtp) cc_final: 0.3469 (mtp) REVERT: B 406 LEU cc_start: 0.4614 (mt) cc_final: 0.3901 (pp) REVERT: B 536 MET cc_start: -0.0176 (tpp) cc_final: -0.0590 (tpp) REVERT: C 33 LEU cc_start: 0.1883 (OUTLIER) cc_final: 0.1423 (tt) REVERT: C 125 MET cc_start: 0.3702 (tpt) cc_final: 0.3068 (mtt) REVERT: C 207 LEU cc_start: 0.3306 (pp) cc_final: 0.2669 (pp) REVERT: C 685 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7577 (pttm) REVERT: D 90 MET cc_start: 0.6918 (ppp) cc_final: 0.6458 (ppp) REVERT: D 133 MET cc_start: -0.0421 (ptm) cc_final: -0.0733 (ptm) REVERT: D 135 MET cc_start: 0.1569 (tmm) cc_final: 0.0811 (mpp) REVERT: D 138 LYS cc_start: -0.0381 (mttp) cc_final: -0.0849 (mttm) REVERT: D 450 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7430 (ppp) outliers start: 49 outliers final: 26 residues processed: 278 average time/residue: 0.1528 time to fit residues: 68.5471 Evaluate side-chains 239 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 95 optimal weight: 0.8980 chunk 266 optimal weight: 50.0000 chunk 4 optimal weight: 0.6980 chunk 314 optimal weight: 50.0000 chunk 88 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 267 optimal weight: 40.0000 chunk 29 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 177 GLN A 196 GLN B 766 GLN C 686 GLN C 780 HIS D 201 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.116991 restraints weight = 139750.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.117169 restraints weight = 93919.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.118087 restraints weight = 82880.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.118508 restraints weight = 62117.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.119099 restraints weight = 43233.093| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4055 moved from start: 0.8555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24028 Z= 0.117 Angle : 0.620 10.930 32848 Z= 0.308 Chirality : 0.041 0.295 3944 Planarity : 0.004 0.068 4283 Dihedral : 4.511 23.214 3494 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.34 % Allowed : 13.42 % Favored : 85.24 % 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: -1.73 (0.16), residues: 2579 helix: 0.13 (0.17), residues: 907 sheet: -1.21 (0.28), residues: 332 loop : -2.10 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 36 TYR 0.029 0.002 TYR A 456 PHE 0.023 0.002 PHE A 197 TRP 0.030 0.002 TRP C 160 HIS 0.012 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00260 (24018) covalent geometry : angle 0.61951 (32830) SS BOND : bond 0.00185 ( 9) SS BOND : angle 0.84850 ( 18) hydrogen bonds : bond 0.02745 ( 935) hydrogen bonds : angle 4.74552 ( 2622) Misc. bond : bond 0.00317 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.4328 (mmm) cc_final: 0.4032 (mmm) REVERT: A 484 PHE cc_start: 0.1916 (OUTLIER) cc_final: 0.0327 (m-80) REVERT: A 518 THR cc_start: 0.3515 (p) cc_final: 0.3288 (t) REVERT: A 696 GLN cc_start: 0.6859 (mt0) cc_final: 0.6575 (mm110) REVERT: A 702 MET cc_start: 0.6761 (mmt) cc_final: 0.6131 (mmm) REVERT: A 765 ASP cc_start: 0.5682 (p0) cc_final: 0.5277 (p0) REVERT: A 778 LYS cc_start: 0.7876 (tptp) cc_final: 0.6901 (tppt) REVERT: B 135 MET cc_start: -0.3091 (ptp) cc_final: -0.3485 (mtt) REVERT: B 242 GLU cc_start: 0.3195 (tp30) cc_final: 0.2877 (tp30) REVERT: B 406 LEU cc_start: 0.5078 (mt) cc_final: 0.4279 (pp) REVERT: C 33 LEU cc_start: 0.1920 (OUTLIER) cc_final: 0.1487 (tt) REVERT: C 125 MET cc_start: 0.3008 (tpt) cc_final: 0.2443 (mtt) REVERT: C 207 LEU cc_start: 0.3893 (pp) cc_final: 0.3394 (pp) REVERT: C 470 MET cc_start: 0.6483 (mpp) cc_final: 0.6189 (mpp) REVERT: C 523 ARG cc_start: 0.1990 (mtt180) cc_final: 0.1587 (ptp90) REVERT: C 686 GLN cc_start: 0.7080 (mm110) cc_final: 0.6785 (mp10) REVERT: C 706 MET cc_start: 0.4575 (ppp) cc_final: 0.3768 (ppp) REVERT: C 784 PHE cc_start: 0.5795 (t80) cc_final: 0.5272 (t80) REVERT: D 112 MET cc_start: 0.2264 (mmt) cc_final: 0.0680 (tpt) REVERT: D 138 LYS cc_start: -0.0853 (mttp) cc_final: -0.1094 (mttm) REVERT: D 315 GLU cc_start: 0.1289 (OUTLIER) cc_final: 0.1061 (pm20) REVERT: D 701 MET cc_start: 0.2139 (tpt) cc_final: 0.1114 (mtt) outliers start: 28 outliers final: 16 residues processed: 242 average time/residue: 0.1463 time to fit residues: 56.5122 Evaluate side-chains 213 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 213 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 313 optimal weight: 50.0000 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 153 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** 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 = 0.4656 r_free = 0.4656 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.114452 restraints weight = 141937.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.113968 restraints weight = 95205.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.114742 restraints weight = 83409.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.115082 restraints weight = 61055.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.115687 restraints weight = 40660.954| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 moved from start: 0.9594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24028 Z= 0.138 Angle : 0.660 13.234 32848 Z= 0.331 Chirality : 0.042 0.303 3944 Planarity : 0.005 0.095 4283 Dihedral : 4.560 22.300 3494 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.53 % Allowed : 13.80 % Favored : 84.67 % 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: -1.71 (0.16), residues: 2579 helix: 0.13 (0.17), residues: 902 sheet: -1.26 (0.27), residues: 354 loop : -2.04 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 36 TYR 0.020 0.002 TYR C 692 PHE 0.040 0.002 PHE B 310 TRP 0.040 0.002 TRP A 792 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00306 (24018) covalent geometry : angle 0.65998 (32830) SS BOND : bond 0.00269 ( 9) SS BOND : angle 1.16375 ( 18) hydrogen bonds : bond 0.03021 ( 935) hydrogen bonds : angle 4.83359 ( 2622) Misc. bond : bond 0.00314 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.3939 (mmm) cc_final: 0.3559 (mmm) REVERT: A 354 MET cc_start: -0.0581 (mtm) cc_final: -0.1658 (mmm) REVERT: A 410 TYR cc_start: 0.2317 (OUTLIER) cc_final: 0.1945 (m-80) REVERT: A 484 PHE cc_start: 0.3983 (OUTLIER) cc_final: 0.2657 (m-80) REVERT: A 501 MET cc_start: 0.5647 (mpp) cc_final: 0.5267 (mpp) REVERT: A 506 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5725 (tt) REVERT: A 702 MET cc_start: 0.6641 (mmt) cc_final: 0.5903 (mmm) REVERT: A 765 ASP cc_start: 0.5788 (p0) cc_final: 0.5195 (p0) REVERT: A 778 LYS cc_start: 0.7746 (tptp) cc_final: 0.7329 (tppt) REVERT: B 135 MET cc_start: -0.2875 (ptp) cc_final: -0.3193 (mtt) REVERT: B 242 GLU cc_start: 0.3183 (tp30) cc_final: 0.2862 (tp30) REVERT: B 406 LEU cc_start: 0.5042 (mt) cc_final: 0.4471 (pp) REVERT: C 33 LEU cc_start: 0.1898 (OUTLIER) cc_final: 0.1526 (tt) REVERT: C 43 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7988 (ptp-170) REVERT: C 125 MET cc_start: 0.3357 (tpt) cc_final: 0.3068 (mtt) REVERT: C 281 ILE cc_start: 0.6017 (mt) cc_final: 0.5812 (mt) REVERT: C 685 LYS cc_start: 0.7852 (ptpp) cc_final: 0.6647 (ptpp) REVERT: C 706 MET cc_start: 0.4453 (ppp) cc_final: 0.3650 (ppp) REVERT: D 112 MET cc_start: 0.2251 (mmt) cc_final: 0.0732 (tpt) REVERT: D 133 MET cc_start: -0.0761 (ptm) cc_final: -0.1353 (ptm) REVERT: D 138 LYS cc_start: -0.0662 (mttp) cc_final: -0.0906 (mttp) REVERT: D 450 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6905 (ppp) REVERT: D 701 MET cc_start: 0.2481 (tpt) cc_final: 0.1494 (mtt) outliers start: 32 outliers final: 20 residues processed: 247 average time/residue: 0.1380 time to fit residues: 56.1721 Evaluate side-chains 226 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 178 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 332 optimal weight: 50.0000 chunk 263 optimal weight: 40.0000 chunk 269 optimal weight: 50.0000 chunk 289 optimal weight: 50.0000 chunk 300 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 chunk 321 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 525 GLN B 85 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 485 HIS B 709 ASN C 101 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 HIS D 709 ASN ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.104445 restraints weight = 121990.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.103137 restraints weight = 101286.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.103918 restraints weight = 75243.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.104465 restraints weight = 59206.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.104906 restraints weight = 50651.710| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5201 moved from start: 1.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.193 24028 Z= 0.307 Angle : 1.070 16.639 32848 Z= 0.556 Chirality : 0.056 0.438 3944 Planarity : 0.008 0.128 4283 Dihedral : 7.002 38.402 3494 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.65 % Favored : 90.27 % Rotamer: Outliers : 2.10 % Allowed : 15.28 % Favored : 82.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.11 (0.15), residues: 2579 helix: -1.43 (0.15), residues: 886 sheet: -2.01 (0.26), residues: 338 loop : -2.56 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 244 TYR 0.047 0.004 TYR B 737 PHE 0.055 0.005 PHE D 186 TRP 0.050 0.004 TRP C 768 HIS 0.018 0.003 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00674 (24018) covalent geometry : angle 1.06802 (32830) SS BOND : bond 0.01440 ( 9) SS BOND : angle 3.22874 ( 18) hydrogen bonds : bond 0.05541 ( 935) hydrogen bonds : angle 6.74660 ( 2622) Misc. bond : bond 0.00359 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.3322 (OUTLIER) cc_final: 0.2076 (ptt180) REVERT: A 108 SER cc_start: 0.8779 (p) cc_final: 0.8572 (t) REVERT: A 180 LEU cc_start: 0.8537 (tt) cc_final: 0.8281 (mp) REVERT: A 354 MET cc_start: -0.0332 (mtm) cc_final: -0.1333 (mmm) REVERT: A 410 TYR cc_start: 0.1046 (OUTLIER) cc_final: 0.0411 (m-80) REVERT: A 412 LYS cc_start: 0.3991 (OUTLIER) cc_final: 0.3636 (pptt) REVERT: A 484 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.3920 (m-80) REVERT: A 778 LYS cc_start: 0.7716 (tptp) cc_final: 0.7177 (tptt) REVERT: B 135 MET cc_start: -0.1291 (ptp) cc_final: -0.1698 (mtt) REVERT: B 306 MET cc_start: 0.2597 (mtp) cc_final: 0.2216 (mtt) REVERT: B 406 LEU cc_start: 0.6798 (mt) cc_final: 0.6509 (mm) REVERT: B 507 MET cc_start: 0.3837 (OUTLIER) cc_final: 0.3494 (mmm) REVERT: C 247 TRP cc_start: 0.1901 (OUTLIER) cc_final: 0.1302 (p90) REVERT: C 702 MET cc_start: 0.3163 (ttt) cc_final: 0.2820 (ttt) REVERT: C 706 MET cc_start: 0.5367 (ppp) cc_final: 0.5072 (ppp) REVERT: D 147 PHE cc_start: -0.0744 (m-80) cc_final: -0.1142 (m-80) REVERT: D 338 MET cc_start: -0.4318 (mmt) cc_final: -0.4635 (mmt) REVERT: D 450 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7234 (ppp) REVERT: D 705 MET cc_start: -0.1241 (ppp) cc_final: -0.1589 (ppp) outliers start: 44 outliers final: 19 residues processed: 287 average time/residue: 0.1455 time to fit residues: 67.0994 Evaluate side-chains 227 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 307 optimal weight: 50.0000 chunk 162 optimal weight: 0.0980 chunk 254 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 324 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.105257 restraints weight = 129886.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.105014 restraints weight = 95732.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.105916 restraints weight = 80003.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.106174 restraints weight = 64118.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.106595 restraints weight = 51087.920| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5058 moved from start: 1.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24028 Z= 0.148 Angle : 0.757 13.551 32848 Z= 0.378 Chirality : 0.044 0.213 3944 Planarity : 0.005 0.106 4283 Dihedral : 5.520 32.077 3494 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.05 % Allowed : 18.19 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.46 (0.15), residues: 2579 helix: -0.69 (0.16), residues: 896 sheet: -1.89 (0.26), residues: 351 loop : -2.26 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 36 TYR 0.022 0.002 TYR A 456 PHE 0.045 0.003 PHE D 186 TRP 0.032 0.002 TRP A 792 HIS 0.020 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00334 (24018) covalent geometry : angle 0.75664 (32830) SS BOND : bond 0.00978 ( 9) SS BOND : angle 1.49672 ( 18) hydrogen bonds : bond 0.03612 ( 935) hydrogen bonds : angle 5.62135 ( 2622) Misc. bond : bond 0.00309 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8370 (t) cc_final: 0.8167 (t) REVERT: A 326 MET cc_start: 0.5598 (mmm) cc_final: 0.5260 (mmm) REVERT: A 354 MET cc_start: -0.0645 (mtm) cc_final: -0.1745 (mmm) REVERT: A 402 THR cc_start: 0.6407 (t) cc_final: 0.6108 (p) REVERT: A 410 TYR cc_start: 0.1317 (OUTLIER) cc_final: 0.0132 (m-80) REVERT: A 412 LYS cc_start: 0.3905 (OUTLIER) cc_final: 0.3648 (pptt) REVERT: A 702 MET cc_start: 0.6955 (mmt) cc_final: 0.6525 (mmm) REVERT: A 778 LYS cc_start: 0.7322 (tptp) cc_final: 0.6860 (tppt) REVERT: B 39 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5668 (mm) REVERT: B 135 MET cc_start: -0.1907 (ptp) cc_final: -0.2120 (mtt) REVERT: B 180 TYR cc_start: 0.4460 (p90) cc_final: 0.4166 (p90) REVERT: B 230 TYR cc_start: 0.4120 (OUTLIER) cc_final: 0.1866 (t80) REVERT: B 234 ASP cc_start: 0.7023 (m-30) cc_final: 0.6728 (m-30) REVERT: B 360 ARG cc_start: 0.2790 (mmm160) cc_final: 0.2349 (mmt-90) REVERT: B 406 LEU cc_start: 0.6771 (mt) cc_final: 0.5810 (pp) REVERT: B 408 ILE cc_start: 0.6927 (mt) cc_final: 0.6385 (mp) REVERT: B 507 MET cc_start: 0.2837 (OUTLIER) cc_final: 0.2360 (mmm) REVERT: C 42 PHE cc_start: 0.7414 (t80) cc_final: 0.7166 (t80) REVERT: C 247 TRP cc_start: 0.2197 (OUTLIER) cc_final: 0.1690 (p90) REVERT: C 287 VAL cc_start: 0.7540 (t) cc_final: 0.7335 (m) REVERT: C 685 LYS cc_start: 0.7441 (ptpp) cc_final: 0.6941 (pttm) REVERT: C 706 MET cc_start: 0.5499 (ppp) cc_final: 0.5242 (ppp) REVERT: C 785 MET cc_start: 0.7446 (pmm) cc_final: 0.7039 (pmm) REVERT: D 112 MET cc_start: 0.4918 (tpp) cc_final: 0.3638 (mpp) REVERT: D 221 LYS cc_start: 0.6626 (pttt) cc_final: 0.6229 (pptt) REVERT: D 248 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2868 (mm) REVERT: D 372 TRP cc_start: -0.1416 (m100) cc_final: -0.1856 (m100) REVERT: D 701 MET cc_start: 0.2061 (tpt) cc_final: 0.1193 (mtt) outliers start: 22 outliers final: 10 residues processed: 239 average time/residue: 0.1492 time to fit residues: 58.5132 Evaluate side-chains 221 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 230 TYR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 795 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 19 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 321 optimal weight: 50.0000 chunk 102 optimal weight: 6.9990 chunk 75 optimal weight: 0.0050 chunk 322 optimal weight: 50.0000 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.131837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.107476 restraints weight = 159688.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 100)---------------| | r_work = 0.4338 r_free = 0.4338 target = 0.106487 restraints weight = 114656.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.106942 restraints weight = 77681.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.107804 restraints weight = 51637.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.107958 restraints weight = 37175.626| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 1.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24028 Z= 0.151 Angle : 0.754 13.401 32848 Z= 0.374 Chirality : 0.043 0.360 3944 Planarity : 0.005 0.093 4283 Dihedral : 5.215 27.340 3494 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.19 % Allowed : 19.01 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.16), residues: 2579 helix: -0.43 (0.17), residues: 891 sheet: -1.61 (0.28), residues: 320 loop : -2.20 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 124 TYR 0.021 0.002 TYR C 474 PHE 0.059 0.003 PHE D 186 TRP 0.048 0.002 TRP A 151 HIS 0.024 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00334 (24018) covalent geometry : angle 0.75336 (32830) SS BOND : bond 0.00320 ( 9) SS BOND : angle 1.00973 ( 18) hydrogen bonds : bond 0.03483 ( 935) hydrogen bonds : angle 5.45639 ( 2622) Misc. bond : bond 0.00306 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4902.00 seconds wall clock time: 84 minutes 56.59 seconds (5096.59 seconds total)