Starting phenix.real_space_refine on Fri Jun 5 14:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.map" model { file = "/net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obs_70297/06_2026/9obs_70297.cif" } resolution = 3.18 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= 0.010 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 88 5.16 5 C 13285 2.51 5 N 3646 2.21 5 O 3831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20850 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5275 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1022 Unresolved non-hydrogen angles: 1290 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ASN:plan1': 18, 'ARG:plan': 24, 'HIS:plan': 9, 'GLU:plan': 36, 'GLN:plan1': 13, 'PHE:plan': 10, 'ASP:plan': 21, 'TYR:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 596 Chain: "B" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5167 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 299} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1064 Unresolved non-hydrogen angles: 1340 Unresolved non-hydrogen dihedrals: 877 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'ASP:plan': 35, 'GLU:plan': 37, 'HIS:plan': 9, 'PHE:plan': 14, 'ARG:plan': 12, 'ASN:plan1': 13, 'GLN:plan1': 14, 'TYR:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 616 Chain: "C" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5160 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1449 Unresolved non-hydrogen dihedrals: 935 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASN:plan1': 24, 'ARG:plan': 26, 'HIS:plan': 10, 'GLU:plan': 34, 'GLN:plan1': 16, 'PHE:plan': 12, 'ASP:plan': 23, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 679 Chain: "D" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5190 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1044 Unresolved non-hydrogen angles: 1317 Unresolved non-hydrogen dihedrals: 866 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ASP:plan': 36, 'GLU:plan': 37, 'HIS:plan': 9, 'PHE:plan': 12, 'ARG:plan': 10, 'ASN:plan1': 12, 'GLN:plan1': 14, 'TYR:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 603 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.29 Number of scatterers: 20850 At special positions: 0 Unit cell: (119.915, 141.417, 172.016, 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 88 16.00 O 3831 8.00 N 3646 7.00 C 13285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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=2.02 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 31 sheets defined 44.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.851A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.505A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.817A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.623A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.539A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.579A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.947A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.551A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.534A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.115A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.712A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.750A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.701A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.869A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.584A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 4.105A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 4.016A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.572A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 838 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.251A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.633A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.217A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.883A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.924A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.556A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 4.048A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.863A pdb=" N LEU B 335 " --> pdb=" O GLN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.528A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 removed outlier: 3.556A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.503A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 3.579A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.531A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.749A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.560A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.708A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.569A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.572A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.733A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.513A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.626A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.157A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.501A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.517A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.569A pdb=" N GLU C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.753A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.538A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.056A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.966A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.623A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 4.088A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.507A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.611A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.628A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.619A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.926A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.941A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 779 " --> pdb=" O SER C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 838 removed outlier: 5.840A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.505A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.781A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.958A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.678A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 removed outlier: 3.585A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.802A pdb=" N TYR D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.588A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.505A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.501A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 706 removed outlier: 3.592A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 710 removed outlier: 3.705A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.730A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 739 " --> pdb=" O VAL D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 755 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.618A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.665A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 845 removed outlier: 5.711A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 removed outlier: 7.403A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.178A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.919A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 478 removed outlier: 6.087A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA9, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.917A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 540 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLU A 751 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 542 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 749 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.231A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 378 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 410 removed outlier: 8.025A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.366A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.496A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.629A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AC1, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.789A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.940A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.533A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 412 removed outlier: 3.598A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.947A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.584A pdb=" N VAL D 71 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.460A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 410 removed outlier: 3.673A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 480 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN D 437 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 451 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.572A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN D 495 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD3, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.682A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3030 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: 4.34 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4472 1.33 - 1.45: 4663 1.45 - 1.57: 11946 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 21227 Sorted by residual: bond pdb=" N THR D 250 " pdb=" CA THR D 250 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.03e+01 bond pdb=" N GLY C 537 " pdb=" CA GLY C 537 " ideal model delta sigma weight residual 1.447 1.475 -0.029 1.01e-02 9.80e+03 8.15e+00 bond pdb=" N LYS D 380 " pdb=" CA LYS D 380 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.08e+00 bond pdb=" N ILE D 730 " pdb=" CA ILE D 730 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" N GLN A 556 " pdb=" CA GLN A 556 " ideal model delta sigma weight residual 1.461 1.485 -0.024 9.20e-03 1.18e+04 6.63e+00 ... (remaining 21222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 28574 1.57 - 3.14: 458 3.14 - 4.70: 67 4.70 - 6.27: 8 6.27 - 7.84: 2 Bond angle restraints: 29109 Sorted by residual: angle pdb=" N PHE C 533 " pdb=" CA PHE C 533 " pdb=" C PHE C 533 " ideal model delta sigma weight residual 113.38 108.81 4.57 1.23e+00 6.61e-01 1.38e+01 angle pdb=" CA PHE C 533 " pdb=" CB PHE C 533 " pdb=" CG PHE C 533 " ideal model delta sigma weight residual 113.80 117.48 -3.68 1.00e+00 1.00e+00 1.36e+01 angle pdb=" N ALA B 734 " pdb=" CA ALA B 734 " pdb=" C ALA B 734 " ideal model delta sigma weight residual 113.50 109.40 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" CA THR C 539 " pdb=" C THR C 539 " pdb=" O THR C 539 " ideal model delta sigma weight residual 121.40 117.71 3.69 1.11e+00 8.12e-01 1.10e+01 angle pdb=" CA GLY C 537 " pdb=" C GLY C 537 " pdb=" O GLY C 537 " ideal model delta sigma weight residual 121.46 117.69 3.77 1.15e+00 7.56e-01 1.08e+01 ... (remaining 29104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 11898 17.66 - 35.31: 428 35.31 - 52.97: 80 52.97 - 70.62: 14 70.62 - 88.28: 10 Dihedral angle restraints: 12430 sinusoidal: 3330 harmonic: 9100 Sorted by residual: dihedral pdb=" CA GLU D 413 " pdb=" C GLU D 413 " pdb=" N ALA D 414 " pdb=" CA ALA D 414 " ideal model delta harmonic sigma weight residual 180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU B 413 " pdb=" C GLU B 413 " pdb=" N ALA B 414 " pdb=" CA ALA B 414 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA THR C 550 " pdb=" C THR C 550 " pdb=" N LEU C 551 " pdb=" CA LEU C 551 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2522 0.042 - 0.085: 781 0.085 - 0.127: 225 0.127 - 0.170: 18 0.170 - 0.212: 1 Chirality restraints: 3547 Sorted by residual: chirality pdb=" CA ILE D 730 " pdb=" N ILE D 730 " pdb=" C ILE D 730 " pdb=" CB ILE D 730 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA TYR B 731 " pdb=" N TYR B 731 " pdb=" C TYR B 731 " pdb=" CB TYR B 731 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE B 534 " pdb=" N ILE B 534 " pdb=" C ILE B 534 " pdb=" CB ILE B 534 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 3544 not shown) Planarity restraints: 3776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 678 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO B 679 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 269 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 270 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 446 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO C 447 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 447 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 447 " 0.022 5.00e-02 4.00e+02 ... (remaining 3773 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 72 2.55 - 3.14: 16783 3.14 - 3.72: 31218 3.72 - 4.31: 41243 4.31 - 4.90: 71673 Nonbonded interactions: 160989 Sorted by model distance: nonbonded pdb=" O ASN B 192 " pdb=" OD1 ASN B 192 " model vdw 1.962 3.040 nonbonded pdb=" OH TYR B 507 " pdb=" OG SER B 770 " model vdw 2.214 3.040 nonbonded pdb=" O ILE A 664 " pdb=" OG1 THR A 749 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN D 180 " pdb=" OD1 ASN D 184 " model vdw 2.246 3.120 nonbonded pdb=" O PHE B 241 " pdb=" ND2 ASN B 245 " model vdw 2.263 3.120 ... (remaining 160984 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 145 and (name N or name CA or name C or name O \ or name CB )) or resid 146 through 156 or (resid 157 through 159 and (name N or \ name CA or name C or name O or name CB )) or resid 160 or (resid 161 and (name \ N or name CA or name C or name O or name CB )) or resid 162 through 168 or (resi \ d 169 through 172 and (name N or name CA or name C or name O or name CB )) or re \ sid 173 through 188 or (resid 189 through 193 and (name N or name CA or name C o \ r name O or name CB )) or resid 194 through 195 or (resid 196 and (name N or nam \ e CA or name C or name O or name CB )) or resid 197 through 200 or (resid 201 th \ rough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 223 or (resid 224 through 229 and (name N or name CA or name C or name O \ or name CB )) or resid 230 through 240 or (resid 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 and (name N or name CA \ or name C or name O or name CB )) or resid 244 through 251 or (resid 252 and (n \ ame N or name CA or name C or name O or name CB )) or resid 253 through 254 or ( \ resid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 \ or (resid 257 through 258 and (name N or name CA or name C or name O or name CB \ )) or resid 259 through 263 or (resid 264 and (name N or name CA or name C or na \ me O or name CB )) or resid 265 through 269 or (resid 270 and (name N or name CA \ or name C or name O or name CB )) or resid 271 through 353 or (resid 354 throug \ h 355 and (name N or name CA or name C or name O or name CB )) or resid 356 or ( \ resid 357 through 361 and (name N or name CA or name C or name O or name CB )) o \ r resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB \ )) or resid 364 through 366 or (resid 367 through 368 and (name N or name CA or \ name C or name O or name CB )) or resid 369 or (resid 370 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 throug \ h 378 and (name N or name CA or name C or name O or name CB )) or resid 379 thro \ ugh 385 or (resid 386 through 387 and (name N or name CA or name C or name O or \ name CB )) or resid 388 through 391 or (resid 392 through 393 and (name N or nam \ e CA or name C or name O or name CB )) or resid 394 through 448 or (resid 449 an \ d (name N or name CA or name C or name O or name CB )) or resid 450 through 480 \ or (resid 481 and (name N or name CA or name C or name O or name CB )) or resid \ 482 through 544 or (resid 545 through 546 and (name N or name CA or name C or na \ me O or name CB )) or resid 547 through 548 or (resid 549 through 553 and (name \ N or name CA or name C or name O or name CB )) or resid 554 through 572 or (resi \ d 573 through 603 and (name N or name CA or name C or name O or name CB )) or re \ sid 604 through 626 or (resid 627 through 629 and (name N or name CA or name C o \ r name O or name CB )) or resid 630 through 694 or (resid 695 and (name N or nam \ e CA or name C or name O or name CB )) or resid 696 through 736 or (resid 737 an \ d (name N or name CA or name C or name O or name CB )) or resid 738 through 770 \ or (resid 771 and (name N or name CA or name C or name O or name CB )) or resid \ 772 through 796 or (resid 797 and (name N or name CA or name C or name O or name \ CB )) or resid 798 through 809 or (resid 810 through 812 and (name N or name CA \ or name C or name O or name CB )) or resid 813 through 819 or (resid 820 throug \ h 821 and (name N or name CA or name C or name O or name CB )) or resid 822 thro \ ugh 901)) selection = (chain 'C' and (resid 25 through 173 or (resid 174 through 176 and (name N or na \ me CA or name C or name O or name CB )) or resid 177 through 392 or (resid 393 a \ nd (name N or name CA or name C or name O or name CB )) or resid 394 through 405 \ or (resid 406 and (name N or name CA or name C or name O or name CB )) or resid \ 407 through 421 or (resid 422 through 423 and (name N or name CA or name C or n \ ame O or name CB )) or resid 424 through 428 or (resid 429 and (name N or name C \ A or name C or name O or name CB )) or resid 430 through 445 or (resid 446 and ( \ name N or name CA or name C or name O or name CB )) or resid 447 through 474 or \ (resid 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 551 or (resid 552 through 553 and (name N or name CA or name C or name \ O or name CB )) or resid 554 through 558 or (resid 559 and (name N or name CA or \ name C or name O or name CB )) or resid 560 through 564 or (resid 565 and (name \ N or name CA or name C or name O or name CB )) or resid 566 through 584 or (res \ id 602 through 603 and (name N or name CA or name C or name O or name CB )) or r \ esid 604 through 659 or (resid 660 through 662 and (name N or name CA or name C \ or name O or name CB )) or resid 663 through 706 or (resid 707 and (name N or na \ me CA or name C or name O or name CB )) or resid 708 through 901)) } ncs_group { reference = (chain 'B' and ((resid 34 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 through 151 or (resid 152 and (name N or name CA or \ name C or name O or name CB )) or resid 153 through 162 or (resid 163 and (name \ N or name CA or name C or name O or name CB )) or resid 164 or (resid 165 and (n \ ame N or name CA or name C or name O or name CB )) or resid 166 through 180 or ( \ resid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ through 191 or (resid 192 and (name N or name CA or name C or name O or name CB \ )) or resid 193 through 207 or (resid 208 through 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 233 or (resid 234 through 23 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 244 or (resid 245 through 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 271 or (resid 272 and (name N or name CA or name \ C or name O or name CB )) or resid 273 through 282 or (resid 283 through 287 an \ d (name N or name CA or name C or name O or name CB )) or (resid 288 through 361 \ and (name N or name CA or name C or name O or name CB )) or resid 362 through 4 \ 24 or (resid 425 and (name N or name CA or name C or name O or name CB )) or res \ id 426 through 429 or (resid 430 and (name N or name CA or name C or name O or n \ ame CB )) or resid 431 through 462 or (resid 463 and (name N or name CA or name \ C or name O or name CB )) or resid 464 through 544 or (resid 545 through 549 and \ (name N or name CA or name C or name O or name CB )) or resid 550 through 601 o \ r (resid 602 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 03 through 785 or (resid 786 and (name N or name CA or name C or name O or name \ CB )) or resid 787 through 810 or (resid 811 and (name N or name CA or name C or \ name O or name CB )) or resid 812 through 901)) selection = (chain 'D' and (resid 34 through 179 or (resid 180 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 215 or (resid 216 t \ hrough 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 235 or (resid 236 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 251 or (resid 252 and (name N or name CA or \ name C or name O or name CB )) or resid 253 through 267 or (resid 268 and (name \ N or name CA or name C or name O or name CB )) or resid 269 through 374 or (res \ id 375 and (name N or name CA or name C or name O or name CB )) or resid 376 thr \ ough 441 or (resid 442 through 449 and (name N or name CA or name C or name O or \ name CB )) or resid 450 through 490 or (resid 491 and (name N or name CA or nam \ e C or name O or name CB )) or resid 492 through 520 or (resid 521 and (name N o \ r name CA or name C or name O or name CB )) or resid 522 through 523 or (resid 5 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 541 or (resid 542 and (name N or name CA or name C or name O or name CB )) or ( \ resid 543 through 549 and (name N or name CA or name C or name O or name CB )) o \ r resid 550 or (resid 551 through 552 and (name N or name CA or name C or name O \ or name CB )) or resid 553 through 559 or (resid 560 through 579 and (name N or \ name CA or name C or name O or name CB )) or resid 600 through 605 or (resid 60 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 607 through \ 621 or (resid 622 and (name N or name CA or name C or name O or name CB )) or re \ sid 623 through 630 or (resid 631 and (name N or name CA or name C or name O or \ name CB )) or resid 632 through 659 or (resid 660 through 662 and (name N or nam \ e CA or name C or name O or name CB )) or resid 663 through 675 or (resid 676 an \ d (name N or name CA or name C or name O or name CB )) or resid 677 through 711 \ or (resid 712 and (name N or name CA or name C or name O or name CB )) or resid \ 713 through 715 or (resid 716 through 717 and (name N or name CA or name C or na \ me O or name CB )) or resid 718 through 726 or (resid 727 through 728 and (name \ N or name CA or name C or name O or name CB )) or resid 729 through 746 or (resi \ d 747 and (name N or name CA or name C or name O or name CB )) or resid 748 thro \ ugh 831 or (resid 832 through 845 and (name N or name CA or name C or name O or \ name CB )) or resid 901)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.030 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 0.050 21239 Z= 0.229 Angle : 0.516 7.838 29133 Z= 0.302 Chirality : 0.044 0.212 3547 Planarity : 0.003 0.059 3776 Dihedral : 10.462 88.276 6506 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.59 % Favored : 93.19 % Rotamer: Outliers : 0.84 % Allowed : 3.96 % Favored : 95.20 % 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: -1.22 (0.15), residues: 3126 helix: 0.16 (0.14), residues: 1283 sheet: -1.70 (0.28), residues: 350 loop : -1.40 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.027 0.001 TYR B 731 PHE 0.020 0.002 PHE A 533 TRP 0.011 0.001 TRP D 379 HIS 0.003 0.001 HIS D 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (21227) covalent geometry : angle 0.51620 / 0.30 (29109) SS BOND : bond 0.00267 / 0.16 ( 12) SS BOND : angle 0.67290 / 0.44 ( 24) hydrogen bonds : bond 0.25730 / 18.66 ( 1044) hydrogen bonds : angle 7.98054 / 5.90 ( 3030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 318 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8011 (mmm) cc_final: 0.7757 (mmm) REVERT: A 545 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7035 (mm-30) REVERT: B 423 ASP cc_start: 0.7219 (t0) cc_final: 0.6943 (t0) REVERT: C 395 SER cc_start: 0.9126 (m) cc_final: 0.8834 (p) REVERT: C 745 ASP cc_start: 0.8244 (t0) cc_final: 0.7862 (t0) REVERT: D 438 LYS cc_start: 0.8292 (tttm) cc_final: 0.7971 (tttp) REVERT: D 477 ASP cc_start: 0.8617 (p0) cc_final: 0.8325 (p0) outliers start: 13 outliers final: 6 residues processed: 329 average time/residue: 0.1300 time to fit residues: 71.6952 Evaluate side-chains 268 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN B 153 GLN B 694 ASN C 177 GLN C 536 GLN C 696 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN D 767 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108346 restraints weight = 27050.603| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.64 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21239 Z= 0.153 Angle : 0.513 8.871 29133 Z= 0.283 Chirality : 0.044 0.170 3547 Planarity : 0.004 0.063 3776 Dihedral : 4.457 47.200 3352 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.47 % Rotamer: Outliers : 1.43 % Allowed : 9.21 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3126 helix: 1.14 (0.14), residues: 1302 sheet: -1.55 (0.27), residues: 353 loop : -1.34 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 431 TYR 0.017 0.001 TYR B 479 PHE 0.026 0.001 PHE B 550 TRP 0.014 0.001 TRP D 379 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (21227) covalent geometry : angle 0.50965 / 0.28 (29109) SS BOND : bond 0.00351 / 0.20 ( 12) SS BOND : angle 2.17668 / 1.37 ( 24) hydrogen bonds : bond 0.04837 / 3.48 ( 1044) hydrogen bonds : angle 5.05745 / 3.72 ( 3030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.726 Fit side-chains REVERT: A 257 ASN cc_start: 0.6895 (t0) cc_final: 0.6480 (t0) REVERT: A 261 TYR cc_start: 0.7488 (m-80) cc_final: 0.7236 (m-80) REVERT: A 354 MET cc_start: 0.7861 (mmm) cc_final: 0.7541 (mmm) REVERT: A 545 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7099 (mm-30) REVERT: A 732 ASP cc_start: 0.8905 (p0) cc_final: 0.8423 (m-30) REVERT: B 653 PHE cc_start: 0.7948 (m-80) cc_final: 0.7512 (m-80) REVERT: B 793 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8467 (mt-10) REVERT: C 707 GLU cc_start: 0.8642 (tp30) cc_final: 0.8404 (tp30) REVERT: C 745 ASP cc_start: 0.8277 (t0) cc_final: 0.7884 (t0) REVERT: C 787 ASP cc_start: 0.7484 (m-30) cc_final: 0.7277 (m-30) REVERT: D 777 ASP cc_start: 0.8195 (m-30) cc_final: 0.7921 (m-30) outliers start: 22 outliers final: 14 residues processed: 287 average time/residue: 0.1172 time to fit residues: 58.6704 Evaluate side-chains 265 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 237 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 ASN D 180 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107936 restraints weight = 27194.606| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.99 r_work: 0.3098 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21239 Z= 0.174 Angle : 0.495 10.311 29133 Z= 0.269 Chirality : 0.043 0.172 3547 Planarity : 0.004 0.064 3776 Dihedral : 4.165 40.958 3344 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 2.20 % Allowed : 10.51 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3126 helix: 1.46 (0.14), residues: 1314 sheet: -1.57 (0.27), residues: 356 loop : -1.34 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 693 TYR 0.016 0.001 TYR B 479 PHE 0.025 0.002 PHE B 550 TRP 0.014 0.001 TRP D 379 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (21227) covalent geometry : angle 0.49140 / 0.27 (29109) SS BOND : bond 0.00385 / 0.26 ( 12) SS BOND : angle 2.09031 / 1.41 ( 24) hydrogen bonds : bond 0.04218 / 3.03 ( 1044) hydrogen bonds : angle 4.60217 / 3.40 ( 3030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.823 Fit side-chains REVERT: A 257 ASN cc_start: 0.6985 (t0) cc_final: 0.6499 (t0) REVERT: A 261 TYR cc_start: 0.7444 (m-80) cc_final: 0.7184 (m-80) REVERT: A 354 MET cc_start: 0.7607 (mmm) cc_final: 0.7180 (mmm) REVERT: A 545 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 732 ASP cc_start: 0.8781 (p0) cc_final: 0.8321 (m-30) REVERT: A 789 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8265 (t0) REVERT: C 395 SER cc_start: 0.9075 (m) cc_final: 0.8794 (p) REVERT: C 475 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7976 (pt0) REVERT: C 536 GLN cc_start: 0.8505 (pp30) cc_final: 0.7933 (pp30) REVERT: C 650 ASN cc_start: 0.8726 (t0) cc_final: 0.8516 (t0) REVERT: C 707 GLU cc_start: 0.8561 (tp30) cc_final: 0.8309 (tp30) REVERT: C 745 ASP cc_start: 0.8193 (t0) cc_final: 0.7835 (t0) REVERT: D 180 GLN cc_start: 0.7810 (tp40) cc_final: 0.7473 (tp-100) REVERT: D 184 ASN cc_start: 0.8340 (m-40) cc_final: 0.7969 (m-40) REVERT: D 477 ASP cc_start: 0.8487 (p0) cc_final: 0.8190 (p0) REVERT: D 777 ASP cc_start: 0.7992 (m-30) cc_final: 0.7711 (m-30) outliers start: 34 outliers final: 20 residues processed: 291 average time/residue: 0.1160 time to fit residues: 58.5218 Evaluate side-chains 276 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 196 optimal weight: 6.9990 chunk 304 optimal weight: 0.3980 chunk 229 optimal weight: 0.7980 chunk 159 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 299 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS D 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110538 restraints weight = 27029.355| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.00 r_work: 0.3130 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21239 Z= 0.112 Angle : 0.445 10.269 29133 Z= 0.242 Chirality : 0.042 0.161 3547 Planarity : 0.003 0.066 3776 Dihedral : 3.941 40.960 3344 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.91 % Rotamer: Outliers : 2.20 % Allowed : 11.93 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 3126 helix: 1.84 (0.15), residues: 1310 sheet: -1.43 (0.26), residues: 367 loop : -1.27 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 693 TYR 0.012 0.001 TYR B 479 PHE 0.026 0.001 PHE B 550 TRP 0.014 0.001 TRP D 610 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (21227) covalent geometry : angle 0.44130 / 0.24 (29109) SS BOND : bond 0.00290 / 0.23 ( 12) SS BOND : angle 1.92527 / 1.31 ( 24) hydrogen bonds : bond 0.03389 / 2.44 ( 1044) hydrogen bonds : angle 4.25208 / 3.14 ( 3030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 257 ASN cc_start: 0.7017 (t0) cc_final: 0.6549 (t0) REVERT: A 261 TYR cc_start: 0.7414 (m-80) cc_final: 0.7168 (m-80) REVERT: A 354 MET cc_start: 0.7465 (mmm) cc_final: 0.7202 (mmm) REVERT: A 400 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (mt) REVERT: A 545 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 695 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7554 (mmt180) REVERT: A 732 ASP cc_start: 0.8639 (p0) cc_final: 0.8387 (m-30) REVERT: B 365 ILE cc_start: 0.9208 (pt) cc_final: 0.8886 (pt) REVERT: C 707 GLU cc_start: 0.8521 (tp30) cc_final: 0.8307 (tp30) REVERT: C 745 ASP cc_start: 0.7921 (t0) cc_final: 0.7622 (t0) REVERT: D 180 GLN cc_start: 0.7704 (tp40) cc_final: 0.7361 (tp-100) REVERT: D 423 ASP cc_start: 0.7826 (t70) cc_final: 0.7600 (m-30) REVERT: D 477 ASP cc_start: 0.8378 (p0) cc_final: 0.8133 (p0) REVERT: D 777 ASP cc_start: 0.8009 (m-30) cc_final: 0.7698 (m-30) REVERT: D 782 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8292 (tp40) outliers start: 34 outliers final: 16 residues processed: 292 average time/residue: 0.1192 time to fit residues: 60.1062 Evaluate side-chains 278 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 422 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 239 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 186 optimal weight: 40.0000 chunk 225 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107359 restraints weight = 27046.981| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.04 r_work: 0.3090 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21239 Z= 0.210 Angle : 0.505 10.196 29133 Z= 0.273 Chirality : 0.044 0.173 3547 Planarity : 0.004 0.064 3776 Dihedral : 4.097 31.970 3344 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.40 % Favored : 93.41 % Rotamer: Outliers : 2.46 % Allowed : 12.65 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 3126 helix: 1.73 (0.15), residues: 1319 sheet: -1.51 (0.27), residues: 361 loop : -1.33 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 671 TYR 0.017 0.001 TYR C 410 PHE 0.027 0.002 PHE B 550 TRP 0.011 0.001 TRP D 610 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (21227) covalent geometry : angle 0.50061 / 0.27 (29109) SS BOND : bond 0.00376 / 0.23 ( 12) SS BOND : angle 2.30573 / 1.47 ( 24) hydrogen bonds : bond 0.03772 / 2.71 ( 1044) hydrogen bonds : angle 4.28245 / 3.16 ( 3030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8459 (t80) cc_final: 0.8088 (t80) REVERT: A 354 MET cc_start: 0.7596 (mmm) cc_final: 0.7179 (mmm) REVERT: A 545 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 732 ASP cc_start: 0.8795 (p0) cc_final: 0.8314 (m-30) REVERT: B 364 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (mm) REVERT: B 365 ILE cc_start: 0.9244 (pt) cc_final: 0.8925 (pt) REVERT: C 395 SER cc_start: 0.9072 (m) cc_final: 0.8815 (p) REVERT: C 475 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: C 745 ASP cc_start: 0.8007 (t0) cc_final: 0.7690 (t0) REVERT: D 180 GLN cc_start: 0.7703 (tp40) cc_final: 0.7253 (tp-100) REVERT: D 184 ASN cc_start: 0.8348 (m-40) cc_final: 0.8049 (m-40) REVERT: D 477 ASP cc_start: 0.8409 (p0) cc_final: 0.8151 (p0) REVERT: D 777 ASP cc_start: 0.8031 (m-30) cc_final: 0.7737 (m-30) outliers start: 38 outliers final: 26 residues processed: 293 average time/residue: 0.1185 time to fit residues: 60.0822 Evaluate side-chains 287 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 111 optimal weight: 0.0050 chunk 176 optimal weight: 1.9990 chunk 264 optimal weight: 50.0000 chunk 185 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 293 optimal weight: 0.8980 chunk 310 optimal weight: 0.0870 chunk 177 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110164 restraints weight = 26868.200| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.64 r_work: 0.3165 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21239 Z= 0.097 Angle : 0.433 9.778 29133 Z= 0.236 Chirality : 0.042 0.166 3547 Planarity : 0.003 0.067 3776 Dihedral : 3.841 34.710 3344 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.23 % Rotamer: Outliers : 1.88 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3126 helix: 2.01 (0.15), residues: 1318 sheet: -1.34 (0.27), residues: 359 loop : -1.27 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 431 TYR 0.012 0.001 TYR A 795 PHE 0.029 0.001 PHE B 550 TRP 0.014 0.001 TRP D 610 HIS 0.002 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (21227) covalent geometry : angle 0.43050 / 0.23 (29109) SS BOND : bond 0.00162 / 0.12 ( 12) SS BOND : angle 1.72726 / 1.17 ( 24) hydrogen bonds : bond 0.03119 / 2.25 ( 1044) hydrogen bonds : angle 4.06191 / 3.01 ( 3030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.872 Fit side-chains REVERT: A 144 TYR cc_start: 0.7959 (m-10) cc_final: 0.7723 (m-10) REVERT: A 354 MET cc_start: 0.7691 (mmm) cc_final: 0.7240 (mmm) REVERT: A 400 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 545 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 695 ARG cc_start: 0.7929 (mmp80) cc_final: 0.7635 (mmt180) REVERT: A 732 ASP cc_start: 0.8785 (p0) cc_final: 0.8518 (m-30) REVERT: B 365 ILE cc_start: 0.9300 (pt) cc_final: 0.8978 (pt) REVERT: C 475 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: C 554 PHE cc_start: 0.7571 (p90) cc_final: 0.7002 (p90) REVERT: C 707 GLU cc_start: 0.8625 (tp30) cc_final: 0.8415 (tp30) REVERT: C 745 ASP cc_start: 0.8050 (t0) cc_final: 0.7693 (t0) REVERT: D 184 ASN cc_start: 0.8347 (m-40) cc_final: 0.8121 (m-40) REVERT: D 777 ASP cc_start: 0.8310 (m-30) cc_final: 0.7988 (m-30) REVERT: D 782 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8407 (tp40) outliers start: 29 outliers final: 22 residues processed: 291 average time/residue: 0.1220 time to fit residues: 61.5620 Evaluate side-chains 288 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 272 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 239 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 164 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 263 optimal weight: 40.0000 chunk 312 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 40.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 ASN D 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108052 restraints weight = 27619.080| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.11 r_work: 0.3113 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21239 Z= 0.220 Angle : 0.507 9.731 29133 Z= 0.274 Chirality : 0.044 0.200 3547 Planarity : 0.004 0.064 3776 Dihedral : 3.999 26.415 3343 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.30 % Favored : 93.51 % Rotamer: Outliers : 2.46 % Allowed : 14.14 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 3126 helix: 1.87 (0.15), residues: 1315 sheet: -1.53 (0.26), residues: 375 loop : -1.32 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 431 TYR 0.017 0.002 TYR C 410 PHE 0.029 0.002 PHE B 550 TRP 0.012 0.001 TRP D 610 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (21227) covalent geometry : angle 0.50337 / 0.27 (29109) SS BOND : bond 0.00351 / 0.20 ( 12) SS BOND : angle 2.12108 / 1.35 ( 24) hydrogen bonds : bond 0.03607 / 2.60 ( 1044) hydrogen bonds : angle 4.15355 / 3.07 ( 3030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.760 Fit side-chains REVERT: A 152 PHE cc_start: 0.8479 (t80) cc_final: 0.8095 (t80) REVERT: A 354 MET cc_start: 0.7613 (mmm) cc_final: 0.7188 (mmm) REVERT: A 545 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 732 ASP cc_start: 0.8795 (p0) cc_final: 0.8320 (m-30) REVERT: B 223 LEU cc_start: 0.8326 (mp) cc_final: 0.8092 (mt) REVERT: B 365 ILE cc_start: 0.9244 (pt) cc_final: 0.8902 (pt) REVERT: C 475 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: C 745 ASP cc_start: 0.8069 (t0) cc_final: 0.7762 (t0) REVERT: D 180 GLN cc_start: 0.7699 (tp40) cc_final: 0.7473 (tp-100) REVERT: D 184 ASN cc_start: 0.8353 (m-40) cc_final: 0.8098 (m-40) outliers start: 38 outliers final: 26 residues processed: 286 average time/residue: 0.1174 time to fit residues: 58.4093 Evaluate side-chains 287 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 300 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 224 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.0030 chunk 139 optimal weight: 1.9990 chunk 259 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 253 optimal weight: 0.0770 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110098 restraints weight = 26819.643| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.66 r_work: 0.3160 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21239 Z= 0.092 Angle : 0.441 9.344 29133 Z= 0.239 Chirality : 0.041 0.183 3547 Planarity : 0.003 0.067 3776 Dihedral : 3.789 30.500 3343 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.73 % Favored : 95.07 % Rotamer: Outliers : 1.49 % Allowed : 14.92 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 3126 helix: 2.11 (0.15), residues: 1319 sheet: -1.28 (0.27), residues: 358 loop : -1.28 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 431 TYR 0.013 0.001 TYR A 261 PHE 0.029 0.001 PHE B 550 TRP 0.016 0.001 TRP D 610 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (21227) covalent geometry : angle 0.43586 / 0.24 (29109) SS BOND : bond 0.00421 / 0.29 ( 12) SS BOND : angle 2.28455 / 1.44 ( 24) hydrogen bonds : bond 0.03001 / 2.17 ( 1044) hydrogen bonds : angle 3.96273 / 2.94 ( 3030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.853 Fit side-chains REVERT: A 354 MET cc_start: 0.7669 (mmm) cc_final: 0.7221 (mmm) REVERT: A 545 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7056 (mm-30) REVERT: A 732 ASP cc_start: 0.8794 (p0) cc_final: 0.8529 (m-30) REVERT: B 223 LEU cc_start: 0.8237 (mp) cc_final: 0.7990 (mt) REVERT: B 365 ILE cc_start: 0.9294 (pt) cc_final: 0.8959 (pt) REVERT: C 475 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: C 554 PHE cc_start: 0.7574 (p90) cc_final: 0.7007 (p90) REVERT: C 707 GLU cc_start: 0.8626 (tp30) cc_final: 0.8413 (tp30) REVERT: C 745 ASP cc_start: 0.8182 (t0) cc_final: 0.7925 (t0) REVERT: D 777 ASP cc_start: 0.8274 (m-30) cc_final: 0.7955 (m-30) outliers start: 23 outliers final: 21 residues processed: 283 average time/residue: 0.1193 time to fit residues: 58.8677 Evaluate side-chains 280 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 236 optimal weight: 30.0000 chunk 167 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 chunk 280 optimal weight: 0.0970 chunk 187 optimal weight: 50.0000 chunk 276 optimal weight: 0.0270 chunk 297 optimal weight: 0.0570 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110526 restraints weight = 27147.752| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.94 r_work: 0.3147 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21239 Z= 0.106 Angle : 0.440 9.212 29133 Z= 0.238 Chirality : 0.042 0.156 3547 Planarity : 0.003 0.066 3776 Dihedral : 3.682 28.956 3343 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 1.56 % Allowed : 15.24 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 3126 helix: 2.20 (0.14), residues: 1320 sheet: -1.29 (0.27), residues: 363 loop : -1.25 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 431 TYR 0.012 0.001 TYR D 479 PHE 0.030 0.001 PHE B 550 TRP 0.015 0.001 TRP D 610 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (21227) covalent geometry : angle 0.43658 / 0.24 (29109) SS BOND : bond 0.00241 / 0.18 ( 12) SS BOND : angle 2.04780 / 1.34 ( 24) hydrogen bonds : bond 0.02975 / 2.14 ( 1044) hydrogen bonds : angle 3.88670 / 2.88 ( 3030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.855 Fit side-chains REVERT: A 354 MET cc_start: 0.7416 (mmm) cc_final: 0.7171 (mmm) REVERT: A 545 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6965 (mm-30) REVERT: B 223 LEU cc_start: 0.8268 (mp) cc_final: 0.8058 (mt) REVERT: B 365 ILE cc_start: 0.9228 (pt) cc_final: 0.8889 (pt) REVERT: B 452 TYR cc_start: 0.8402 (m-10) cc_final: 0.8170 (m-80) REVERT: C 475 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: C 554 PHE cc_start: 0.7561 (p90) cc_final: 0.7055 (p90) REVERT: D 777 ASP cc_start: 0.8006 (m-30) cc_final: 0.7655 (m-30) REVERT: D 782 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8366 (tp40) outliers start: 24 outliers final: 22 residues processed: 273 average time/residue: 0.1217 time to fit residues: 57.7472 Evaluate side-chains 274 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 306 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 270 optimal weight: 0.4980 chunk 220 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 112 optimal weight: 0.0000 chunk 237 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN D 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110323 restraints weight = 27115.926| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.15 r_work: 0.3136 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21239 Z= 0.100 Angle : 0.436 9.072 29133 Z= 0.236 Chirality : 0.041 0.150 3547 Planarity : 0.003 0.067 3776 Dihedral : 3.656 35.671 3343 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.61 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 15.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 3126 helix: 2.26 (0.14), residues: 1321 sheet: -1.31 (0.27), residues: 365 loop : -1.24 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 431 TYR 0.015 0.001 TYR D 389 PHE 0.030 0.001 PHE B 550 TRP 0.022 0.001 TRP D 610 HIS 0.002 0.000 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21227) covalent geometry : angle 0.43309 / 0.23 (29109) SS BOND : bond 0.00260 / 0.19 ( 12) SS BOND : angle 1.75501 / 1.17 ( 24) hydrogen bonds : bond 0.02878 / 2.07 ( 1044) hydrogen bonds : angle 3.83660 / 2.85 ( 3030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.910 Fit side-chains REVERT: A 354 MET cc_start: 0.7396 (mmm) cc_final: 0.7073 (mmm) REVERT: A 545 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 756 SER cc_start: 0.8957 (p) cc_final: 0.8745 (m) REVERT: B 223 LEU cc_start: 0.8237 (mp) cc_final: 0.8002 (mt) REVERT: B 365 ILE cc_start: 0.9205 (pt) cc_final: 0.8860 (pt) REVERT: B 452 TYR cc_start: 0.8383 (m-10) cc_final: 0.8155 (m-80) REVERT: C 475 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: C 554 PHE cc_start: 0.7525 (p90) cc_final: 0.7037 (p90) REVERT: D 777 ASP cc_start: 0.8025 (m-30) cc_final: 0.7685 (m-30) REVERT: D 782 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8351 (tp40) outliers start: 24 outliers final: 21 residues processed: 266 average time/residue: 0.1181 time to fit residues: 54.9300 Evaluate side-chains 271 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 227 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN D 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110496 restraints weight = 26993.661| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.04 r_work: 0.3148 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21239 Z= 0.110 Angle : 0.439 9.008 29133 Z= 0.237 Chirality : 0.042 0.151 3547 Planarity : 0.003 0.066 3776 Dihedral : 3.621 27.357 3343 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 1.75 % Allowed : 15.24 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 3126 helix: 2.29 (0.14), residues: 1321 sheet: -1.31 (0.27), residues: 360 loop : -1.22 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 431 TYR 0.016 0.001 TYR D 389 PHE 0.031 0.001 PHE B 550 TRP 0.023 0.001 TRP D 610 HIS 0.003 0.001 HIS D 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (21227) covalent geometry : angle 0.43634 / 0.24 (29109) SS BOND : bond 0.00238 / 0.17 ( 12) SS BOND : angle 1.73154 / 1.16 ( 24) hydrogen bonds : bond 0.02886 / 2.08 ( 1044) hydrogen bonds : angle 3.80828 / 2.82 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6135.47 seconds wall clock time: 105 minutes 11.55 seconds (6311.55 seconds total)