Starting phenix.real_space_refine on Mon Sep 14 11:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.map" model { file = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs7_4626/09_2026/6qs7_4626.cif" } resolution = 3.8 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1218 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 108 5.16 5 C 18010 2.51 5 N 5230 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28875 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.53, per 1000 atoms: 0.23 Number of scatterers: 28875 At special positions: 0 Unit cell: (124.95, 144.9, 157.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 32 15.00 Mg 8 11.99 O 5487 8.00 N 5230 7.00 C 18010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6724 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 29 sheets defined 59.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.963A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.050A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.650A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.736A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.787A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.643A pdb=" N VAL A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 623 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.738A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.535A pdb=" N ARG A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.832A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.512A pdb=" N MET A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.655A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 813 through 827 removed outlier: 4.325A pdb=" N LEU A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.798A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 4.094A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.735A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Proline residue: B 301 - end of helix removed outlier: 4.041A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 removed outlier: 4.046A pdb=" N ARG B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 342 through 362 removed outlier: 5.247A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.771A pdb=" N ILE B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.861A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 Processing helix chain 'B' and resid 641 through 648 Processing helix chain 'B' and resid 660 through 668 Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.929A pdb=" N PHE B 687 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.724A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 Proline residue: B 828 - end of helix removed outlier: 3.555A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.895A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 254 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.677A pdb=" N ARG C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 4.300A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 removed outlier: 3.567A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.731A pdb=" N SER C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 444 through 465 Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.638A pdb=" N ILE C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 561 Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 573 through 590 Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.710A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 669 removed outlier: 4.234A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 682 removed outlier: 4.050A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.762A pdb=" N PHE C 687 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 Processing helix chain 'C' and resid 767 through 790 removed outlier: 3.726A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 807 Processing helix chain 'C' and resid 814 through 825 removed outlier: 3.793A pdb=" N LYS C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 835 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.736A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.562A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.292A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 323 removed outlier: 4.002A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 362 removed outlier: 3.511A pdb=" N THR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 429 Processing helix chain 'D' and resid 444 through 465 Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.843A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.758A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.878A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.616A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 683 through 697 removed outlier: 4.095A pdb=" N PHE D 687 " --> pdb=" O HIS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 removed outlier: 3.734A pdb=" N MET D 737 " --> pdb=" O ASP D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 807 Processing helix chain 'D' and resid 814 through 834 removed outlier: 3.697A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 225 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 241 through 249 removed outlier: 3.915A pdb=" N LEU E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 249' Processing helix chain 'E' and resid 253 through 270 Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 295 through 304 Proline residue: E 301 - end of helix removed outlier: 4.013A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.532A pdb=" N ILE E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.847A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.795A pdb=" N ILE E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 409 through 429 Processing helix chain 'E' and resid 444 through 466 Processing helix chain 'E' and resid 532 through 544 removed outlier: 3.590A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 removed outlier: 3.665A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.566A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 624 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 661 through 669 removed outlier: 3.801A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 733 through 749 removed outlier: 3.513A pdb=" N MET E 737 " --> pdb=" O ASP E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 788 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 814 through 835 removed outlier: 3.527A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.949A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.592A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 295 through 304 Proline residue: F 301 - end of helix removed outlier: 3.774A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.875A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 570 removed outlier: 4.699A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 589 Processing helix chain 'F' and resid 610 through 623 Processing helix chain 'F' and resid 642 through 647 Processing helix chain 'F' and resid 654 through 658 removed outlier: 4.084A pdb=" N GLU F 657 " --> pdb=" O VAL F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 683 through 696 removed outlier: 3.757A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 753 through 757 removed outlier: 3.601A pdb=" N ARG F 756 " --> pdb=" O PHE F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 790 Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 814 through 835 Proline residue: F 828 - end of helix removed outlier: 3.660A pdb=" N LEU F 834 " --> pdb=" O ALA F 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.468A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A 311 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 275 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N THR A 315 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 206 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 removed outlier: 8.134A pdb=" N GLN A 364 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 633 removed outlier: 3.641A pdb=" N PHE A 601 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 700 Processing sheet with id=AA5, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.365A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 311 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 275 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR B 315 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.239A pdb=" N GLN B 364 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.664A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 700 removed outlier: 3.544A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.516A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP C 278 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL C 311 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 275 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.261A pdb=" N ILE C 674 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB5, first strand: chain 'C' and resid 844 through 848 removed outlier: 3.821A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.057A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL D 311 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 275 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA D 313 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 277 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N THR D 315 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 364 through 365 removed outlier: 7.047A pdb=" N GLN D 364 " --> pdb=" O VAL D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.194A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER D 600 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 761 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 602 " --> pdb=" O VAL D 761 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 698 through 700 Processing sheet with id=AC1, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.723A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 165 through 167 removed outlier: 6.202A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU E 240 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL E 311 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU E 275 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA E 313 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 277 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR E 314 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 334 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 203 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.244A pdb=" N GLN E 364 " --> pdb=" O VAL E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.432A pdb=" N SER E 600 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.525A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 846 through 848 Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.822A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL F 311 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 275 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA F 313 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 277 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR F 315 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.047A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 630 through 633 removed outlier: 6.465A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE F 601 " --> pdb=" O MET F 716 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER F 718 " --> pdb=" O PHE F 601 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 603 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 761 " --> pdb=" O LEU F 602 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 699 through 700 Processing sheet with id=AD2, first strand: chain 'F' and resid 792 through 795 removed outlier: 6.936A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) 1463 hydrogen bonds defined for protein. 4299 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: 6.09 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10032 1.34 - 1.50: 7639 1.50 - 1.65: 11433 1.65 - 1.80: 160 1.80 - 1.95: 34 Bond restraints: 29298 Sorted by residual: bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.72e-02 3.38e+03 2.56e+01 bond pdb=" C GLY A 253 " pdb=" N GLU A 254 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" C ALA D 682 " pdb=" N HIS D 683 " ideal model delta sigma weight residual 1.333 1.224 0.108 2.74e-02 1.33e+03 1.56e+01 bond pdb=" C PHE C 749 " pdb=" N ARG C 750 " ideal model delta sigma weight residual 1.333 1.246 0.086 2.74e-02 1.33e+03 9.90e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 ... (remaining 29293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 38556 2.81 - 5.62: 918 5.62 - 8.42: 105 8.42 - 11.23: 15 11.23 - 14.04: 4 Bond angle restraints: 39598 Sorted by residual: angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.48 9.10 1.95e+00 2.63e-01 2.18e+01 angle pdb=" C GLY F 730 " pdb=" N GLU F 731 " pdb=" CA GLU F 731 " ideal model delta sigma weight residual 122.08 128.02 -5.94 1.47e+00 4.63e-01 1.63e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 122.46 111.80 10.66 2.70e+00 1.37e-01 1.56e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 113.18 104.14 9.04 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA LEU E 646 " pdb=" CB LEU E 646 " pdb=" CG LEU E 646 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 17537 23.96 - 47.93: 381 47.93 - 71.89: 28 71.89 - 95.85: 8 95.85 - 119.82: 2 Dihedral angle restraints: 17956 sinusoidal: 7533 harmonic: 10423 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -179.81 119.82 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.25 116.25 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 17953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3091 0.057 - 0.113: 1107 0.113 - 0.170: 252 0.170 - 0.226: 24 0.226 - 0.283: 5 Chirality restraints: 4479 Sorted by residual: chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU B 694 " pdb=" CB LEU B 694 " pdb=" CD1 LEU B 694 " pdb=" CD2 LEU B 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL D 679 " pdb=" CA VAL D 679 " pdb=" CG1 VAL D 679 " pdb=" CG2 VAL D 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4476 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 301 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.013 2.00e-02 2.50e+03 2.18e-02 8.30e+00 pdb=" CG PHE C 763 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 823 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLN C 823 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN C 823 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 824 " 0.016 2.00e-02 2.50e+03 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 352 2.61 - 3.18: 24414 3.18 - 3.76: 44349 3.76 - 4.33: 61439 4.33 - 4.90: 101355 Nonbonded interactions: 231909 Sorted by model distance: nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.041 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.046 2.170 nonbonded pdb=" OG1 THR C 612 " pdb="MG MG C1004 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR D 612 " pdb="MG MG D1004 " model vdw 2.067 2.170 nonbonded pdb=" O1B AGS D1001 " pdb="MG MG D1003 " model vdw 2.067 2.170 ... (remaining 231904 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 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 858)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.890 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.011 0.754 29307 Z= 0.620 Angle : 1.053 14.039 39598 Z= 0.564 Chirality : 0.059 0.283 4479 Planarity : 0.008 0.074 5170 Dihedral : 10.389 119.815 11232 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.20 % Allowed : 0.76 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -3.83 (0.11), residues: 3563 helix: -2.30 (0.09), residues: 1903 sheet: -2.75 (0.25), residues: 339 loop : -2.58 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 332 TYR 0.037 0.003 TYR D 653 PHE 0.043 0.004 PHE C 763 TRP 0.037 0.005 TRP B 543 HIS 0.013 0.002 HIS F 747 Details of bonding type rmsd/Z covalent geometry : bond 0.01052 / 0.44 (29298) covalent geometry : angle 1.05254 / 0.56 (39598) hydrogen bonds : bond 0.16776 / 11.20 ( 1463) hydrogen bonds : angle 7.71386 / 5.39 ( 4299) Misc. bond : bond 0.25136 / 11.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 930 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 TYR cc_start: 0.8656 (m-10) cc_final: 0.7590 (m-10) REVERT: A 326 ASP cc_start: 0.8334 (t70) cc_final: 0.8079 (t0) REVERT: A 564 GLN cc_start: 0.8854 (tt0) cc_final: 0.8317 (tp-100) REVERT: A 642 SER cc_start: 0.7711 (m) cc_final: 0.7277 (p) REVERT: A 671 TYR cc_start: 0.8824 (m-80) cc_final: 0.8620 (m-80) REVERT: A 738 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7288 (pttm) REVERT: A 794 HIS cc_start: 0.7673 (m170) cc_final: 0.7074 (t70) REVERT: A 842 LYS cc_start: 0.4084 (mttt) cc_final: 0.3826 (mmtm) REVERT: B 354 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8171 (tttm) REVERT: B 533 ASP cc_start: 0.7983 (p0) cc_final: 0.7663 (p0) REVERT: B 562 MET cc_start: 0.8927 (tpt) cc_final: 0.8701 (tpt) REVERT: B 634 MET cc_start: 0.9387 (mmm) cc_final: 0.9181 (mmm) REVERT: B 677 ASP cc_start: 0.8035 (t0) cc_final: 0.7530 (t0) REVERT: B 700 THR cc_start: 0.8368 (m) cc_final: 0.7854 (p) REVERT: B 729 PHE cc_start: 0.7758 (t80) cc_final: 0.7128 (t80) REVERT: B 779 LEU cc_start: 0.9279 (mt) cc_final: 0.8961 (mp) REVERT: B 802 LEU cc_start: 0.8709 (mp) cc_final: 0.8219 (pp) REVERT: B 818 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8818 (ttpp) REVERT: B 826 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8421 (mp0) REVERT: C 236 ARG cc_start: 0.8344 (mmt180) cc_final: 0.7967 (mmp80) REVERT: C 241 ASP cc_start: 0.7731 (t0) cc_final: 0.7312 (t0) REVERT: C 246 VAL cc_start: 0.9248 (t) cc_final: 0.8986 (p) REVERT: C 257 GLU cc_start: 0.8393 (tt0) cc_final: 0.8040 (tt0) REVERT: C 334 GLN cc_start: 0.8499 (mm110) cc_final: 0.7885 (mm-40) REVERT: C 388 ASP cc_start: 0.8750 (t70) cc_final: 0.8483 (t0) REVERT: C 423 LYS cc_start: 0.8683 (tptm) cc_final: 0.8383 (ttpt) REVERT: C 532 THR cc_start: 0.8264 (p) cc_final: 0.7997 (m) REVERT: C 692 GLN cc_start: 0.8103 (mt0) cc_final: 0.7650 (mt0) REVERT: C 705 ARG cc_start: 0.7652 (ptt-90) cc_final: 0.7202 (ptp90) REVERT: C 780 LYS cc_start: 0.9083 (mttt) cc_final: 0.8707 (tptt) REVERT: C 786 LEU cc_start: 0.9154 (mt) cc_final: 0.8923 (tp) REVERT: C 801 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8562 (ttpp) REVERT: C 826 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 161 LEU cc_start: 0.8922 (mt) cc_final: 0.8555 (mt) REVERT: D 163 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8557 (mptt) REVERT: D 265 ASP cc_start: 0.8066 (m-30) cc_final: 0.7721 (t0) REVERT: D 330 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 345 ASP cc_start: 0.8374 (m-30) cc_final: 0.7777 (m-30) REVERT: D 552 MET cc_start: 0.7720 (ptm) cc_final: 0.6986 (ppp) REVERT: D 644 SER cc_start: 0.8837 (m) cc_final: 0.8534 (p) REVERT: D 696 ASP cc_start: 0.8757 (m-30) cc_final: 0.8544 (m-30) REVERT: D 780 LYS cc_start: 0.8736 (mttt) cc_final: 0.8221 (mtmm) REVERT: D 827 ASN cc_start: 0.8692 (m-40) cc_final: 0.8064 (m110) REVERT: E 162 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8322 (pttm) REVERT: E 191 ILE cc_start: 0.8699 (mt) cc_final: 0.8398 (mm) REVERT: E 205 ILE cc_start: 0.8775 (mt) cc_final: 0.8396 (pt) REVERT: E 257 GLU cc_start: 0.8923 (tt0) cc_final: 0.8510 (mm-30) REVERT: E 359 LEU cc_start: 0.8970 (mp) cc_final: 0.8690 (mp) REVERT: E 426 GLN cc_start: 0.8706 (tt0) cc_final: 0.8353 (mt0) REVERT: E 458 LEU cc_start: 0.7723 (mt) cc_final: 0.7452 (mt) REVERT: E 568 HIS cc_start: 0.7151 (m170) cc_final: 0.6924 (m-70) REVERT: E 633 ASP cc_start: 0.8844 (m-30) cc_final: 0.8528 (m-30) REVERT: E 634 MET cc_start: 0.9076 (mmm) cc_final: 0.8801 (tpp) REVERT: E 707 VAL cc_start: 0.9405 (t) cc_final: 0.9142 (m) REVERT: E 726 GLN cc_start: 0.7752 (mt0) cc_final: 0.7282 (pt0) REVERT: F 178 ASP cc_start: 0.8100 (m-30) cc_final: 0.7650 (p0) REVERT: F 217 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6709 (mt-10) REVERT: F 330 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7274 (pt0) REVERT: F 335 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8333 (ttmm) REVERT: F 376 LEU cc_start: 0.7946 (mt) cc_final: 0.7688 (pp) REVERT: F 393 LEU cc_start: 0.7670 (mt) cc_final: 0.7196 (mp) REVERT: F 538 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7389 (tp30) REVERT: F 563 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6314 (pt0) REVERT: F 582 ASN cc_start: 0.8946 (m-40) cc_final: 0.8659 (m-40) REVERT: F 595 ASN cc_start: 0.8543 (m-40) cc_final: 0.7792 (t0) REVERT: F 626 ASP cc_start: 0.7472 (m-30) cc_final: 0.6969 (p0) REVERT: F 629 MET cc_start: 0.8167 (ptm) cc_final: 0.7787 (ptp) REVERT: F 630 VAL cc_start: 0.8421 (t) cc_final: 0.7928 (t) REVERT: F 631 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7528 (ttt180) REVERT: F 638 MET cc_start: 0.7561 (mtm) cc_final: 0.7344 (mmm) REVERT: F 691 LEU cc_start: 0.9074 (mt) cc_final: 0.8840 (pp) REVERT: F 736 HIS cc_start: 0.8428 (m170) cc_final: 0.8039 (m-70) REVERT: F 821 ILE cc_start: 0.8900 (mt) cc_final: 0.8326 (mt) outliers start: 6 outliers final: 1 residues processed: 936 average time/residue: 0.2409 time to fit residues: 332.5223 Evaluate side-chains 482 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 201 ASN A 404 GLN A 692 GLN A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN B 297 ASN B 620 ASN B 641 HIS B 692 GLN B 747 HIS B 748 ASN B 822 GLN C 692 GLN C 794 HIS ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN D 192 GLN D 201 ASN D 567 HIS D 641 HIS D 692 GLN D 726 GLN D 748 ASN D 822 GLN E 297 ASN E 309 HIS E 334 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 HIS F 281 HIS F 309 HIS ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 776 GLN F 849 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096770 restraints weight = 56856.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099267 restraints weight = 30957.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100893 restraints weight = 20584.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101910 restraints weight = 15822.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102404 restraints weight = 13487.616| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29307 Z= 0.158 Angle : 0.720 14.321 39598 Z= 0.359 Chirality : 0.045 0.226 4479 Planarity : 0.006 0.061 5170 Dihedral : 7.811 91.042 4099 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.43 % Allowed : 9.04 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3563 helix: -0.78 (0.11), residues: 1941 sheet: -2.49 (0.25), residues: 385 loop : -1.92 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 561 TYR 0.028 0.002 TYR E 380 PHE 0.016 0.002 PHE F 729 TRP 0.023 0.002 TRP D 543 HIS 0.009 0.001 HIS B 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (29298) covalent geometry : angle 0.71988 / 0.36 (39598) hydrogen bonds : bond 0.05119 / 3.47 ( 1463) hydrogen bonds : angle 5.65727 / 3.95 ( 4299) Misc. bond : bond 0.00508 / 0.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 580 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7091 (ttpt) REVERT: A 251 TYR cc_start: 0.8184 (m-10) cc_final: 0.7399 (m-10) REVERT: A 564 GLN cc_start: 0.8657 (tt0) cc_final: 0.8180 (tp-100) REVERT: A 642 SER cc_start: 0.7485 (m) cc_final: 0.7034 (p) REVERT: A 671 TYR cc_start: 0.8562 (m-80) cc_final: 0.8356 (m-80) REVERT: A 692 GLN cc_start: 0.8069 (mt0) cc_final: 0.7757 (mt0) REVERT: A 752 GLU cc_start: 0.7178 (tt0) cc_final: 0.6951 (mt-10) REVERT: A 794 HIS cc_start: 0.7770 (m170) cc_final: 0.7189 (t70) REVERT: A 842 LYS cc_start: 0.3853 (mttt) cc_final: 0.3501 (mmtm) REVERT: B 178 ASP cc_start: 0.7803 (m-30) cc_final: 0.7497 (m-30) REVERT: B 298 MET cc_start: 0.8694 (mtp) cc_final: 0.8433 (mtp) REVERT: B 692 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: B 700 THR cc_start: 0.8730 (m) cc_final: 0.8226 (p) REVERT: B 754 ILE cc_start: 0.9408 (pt) cc_final: 0.9165 (mt) REVERT: B 774 ILE cc_start: 0.9066 (mt) cc_final: 0.8795 (mt) REVERT: B 779 LEU cc_start: 0.9032 (mt) cc_final: 0.8800 (mt) REVERT: B 794 HIS cc_start: 0.6597 (t70) cc_final: 0.6394 (t-90) REVERT: B 808 TYR cc_start: 0.5808 (t80) cc_final: 0.5051 (t80) REVERT: B 817 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8492 (tt) REVERT: C 192 GLN cc_start: 0.8607 (mt0) cc_final: 0.8398 (mt0) REVERT: C 388 ASP cc_start: 0.8639 (t70) cc_final: 0.8429 (t0) REVERT: C 758 ASP cc_start: 0.7939 (m-30) cc_final: 0.7661 (m-30) REVERT: D 161 LEU cc_start: 0.9026 (mt) cc_final: 0.8597 (mt) REVERT: D 163 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8351 (mptt) REVERT: D 345 ASP cc_start: 0.7965 (m-30) cc_final: 0.7614 (m-30) REVERT: D 827 ASN cc_start: 0.8514 (m-40) cc_final: 0.7888 (m110) REVERT: E 162 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8320 (pttm) REVERT: E 185 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: E 329 LEU cc_start: 0.7734 (tp) cc_final: 0.7319 (tp) REVERT: E 707 VAL cc_start: 0.9492 (t) cc_final: 0.9204 (m) REVERT: F 217 GLU cc_start: 0.7876 (mt-10) cc_final: 0.6794 (mt-10) REVERT: F 330 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7108 (pt0) REVERT: F 538 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7597 (tp30) REVERT: F 540 LEU cc_start: 0.7819 (mm) cc_final: 0.7314 (mm) REVERT: F 582 ASN cc_start: 0.8699 (m-40) cc_final: 0.8386 (m-40) REVERT: F 595 ASN cc_start: 0.8197 (m-40) cc_final: 0.7603 (t0) REVERT: F 746 SER cc_start: 0.8654 (m) cc_final: 0.8363 (p) REVERT: F 821 ILE cc_start: 0.9093 (mt) cc_final: 0.8802 (mt) outliers start: 73 outliers final: 36 residues processed: 626 average time/residue: 0.2009 time to fit residues: 197.6349 Evaluate side-chains 479 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 440 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 748 ASN C 794 HIS D 281 HIS D 857 GLN E 309 HIS E 620 ASN F 195 GLN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094833 restraints weight = 57997.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096774 restraints weight = 31109.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097503 restraints weight = 20455.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098088 restraints weight = 18454.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098104 restraints weight = 15608.047| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29307 Z= 0.184 Angle : 0.689 14.572 39598 Z= 0.343 Chirality : 0.045 0.219 4479 Planarity : 0.005 0.057 5170 Dihedral : 7.520 87.326 4099 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.83 % Allowed : 11.54 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -1.45 (0.14), residues: 3563 helix: -0.13 (0.11), residues: 1964 sheet: -2.38 (0.25), residues: 372 loop : -1.69 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 631 TYR 0.021 0.002 TYR D 653 PHE 0.025 0.002 PHE C 729 TRP 0.014 0.002 TRP D 543 HIS 0.016 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (29298) covalent geometry : angle 0.68926 / 0.34 (39598) hydrogen bonds : bond 0.04837 / 3.27 ( 1463) hydrogen bonds : angle 5.29498 / 3.69 ( 4299) Misc. bond : bond 0.00273 / 0.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 465 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7158 (ttpt) REVERT: A 251 TYR cc_start: 0.8222 (m-10) cc_final: 0.7438 (m-10) REVERT: A 564 GLN cc_start: 0.8710 (tt0) cc_final: 0.8212 (tp-100) REVERT: A 641 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5712 (p-80) REVERT: A 642 SER cc_start: 0.7551 (m) cc_final: 0.7293 (p) REVERT: A 794 HIS cc_start: 0.7593 (m170) cc_final: 0.7242 (t70) REVERT: A 842 LYS cc_start: 0.3657 (mttt) cc_final: 0.3379 (mmtm) REVERT: B 178 ASP cc_start: 0.7917 (m-30) cc_final: 0.7620 (m-30) REVERT: B 298 MET cc_start: 0.8691 (mtp) cc_final: 0.8413 (mtp) REVERT: B 581 SER cc_start: 0.9205 (m) cc_final: 0.8692 (p) REVERT: B 754 ILE cc_start: 0.9441 (pt) cc_final: 0.9218 (mt) REVERT: B 774 ILE cc_start: 0.9128 (mt) cc_final: 0.8923 (mt) REVERT: B 808 TYR cc_start: 0.5651 (t80) cc_final: 0.4954 (t80) REVERT: C 241 ASP cc_start: 0.7381 (t0) cc_final: 0.7095 (t0) REVERT: C 421 GLN cc_start: 0.8394 (tp40) cc_final: 0.8031 (tt0) REVERT: D 163 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8285 (mptt) REVERT: D 827 ASN cc_start: 0.8449 (m-40) cc_final: 0.7941 (m110) REVERT: E 162 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8334 (pttm) REVERT: E 454 GLN cc_start: 0.7532 (mm110) cc_final: 0.7280 (mm110) REVERT: E 707 VAL cc_start: 0.9550 (t) cc_final: 0.9217 (m) REVERT: F 330 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7212 (pt0) REVERT: F 563 GLU cc_start: 0.7055 (tp30) cc_final: 0.6812 (tp30) REVERT: F 582 ASN cc_start: 0.8699 (m-40) cc_final: 0.8417 (m-40) REVERT: F 746 SER cc_start: 0.8718 (m) cc_final: 0.8451 (p) REVERT: F 821 ILE cc_start: 0.9120 (mt) cc_final: 0.8821 (mt) outliers start: 85 outliers final: 53 residues processed: 517 average time/residue: 0.1921 time to fit residues: 158.5222 Evaluate side-chains 441 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 387 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN C 421 GLN E 309 HIS F 195 GLN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.122642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095019 restraints weight = 57858.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097305 restraints weight = 32219.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098788 restraints weight = 21793.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099711 restraints weight = 17028.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100242 restraints weight = 14681.806| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29307 Z= 0.156 Angle : 0.652 15.282 39598 Z= 0.321 Chirality : 0.044 0.228 4479 Planarity : 0.005 0.058 5170 Dihedral : 7.312 86.375 4099 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.52 % Allowed : 12.37 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.95 (0.14), residues: 3563 helix: 0.31 (0.11), residues: 1969 sheet: -2.31 (0.25), residues: 375 loop : -1.48 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 728 TYR 0.028 0.002 TYR B 783 PHE 0.014 0.001 PHE E 621 TRP 0.014 0.002 TRP F 543 HIS 0.004 0.001 HIS E 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (29298) covalent geometry : angle 0.65245 / 0.32 (39598) hydrogen bonds : bond 0.04493 / 3.04 ( 1463) hydrogen bonds : angle 5.08799 / 3.55 ( 4299) Misc. bond : bond 0.00240 / 0.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 435 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7078 (ttpt) REVERT: A 251 TYR cc_start: 0.8216 (m-10) cc_final: 0.7507 (m-10) REVERT: A 564 GLN cc_start: 0.8573 (tt0) cc_final: 0.8167 (tp-100) REVERT: A 641 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.5710 (p-80) REVERT: A 794 HIS cc_start: 0.7714 (m170) cc_final: 0.7213 (t70) REVERT: A 842 LYS cc_start: 0.3847 (mttt) cc_final: 0.3485 (mmtm) REVERT: B 178 ASP cc_start: 0.7914 (m-30) cc_final: 0.7661 (m-30) REVERT: B 298 MET cc_start: 0.8673 (mtp) cc_final: 0.8405 (mtp) REVERT: B 708 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 808 TYR cc_start: 0.5542 (t80) cc_final: 0.5087 (t80) REVERT: C 392 ASP cc_start: 0.8085 (m-30) cc_final: 0.7849 (m-30) REVERT: C 633 ASP cc_start: 0.8435 (t70) cc_final: 0.8175 (t70) REVERT: D 163 LYS cc_start: 0.8499 (mmtm) cc_final: 0.8202 (mmtm) REVERT: D 827 ASN cc_start: 0.8535 (m-40) cc_final: 0.8066 (m110) REVERT: E 162 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8332 (pttm) REVERT: E 562 MET cc_start: 0.6507 (tmm) cc_final: 0.6251 (tmm) REVERT: E 646 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8930 (pt) REVERT: E 707 VAL cc_start: 0.9543 (t) cc_final: 0.9246 (m) REVERT: F 540 LEU cc_start: 0.7728 (mm) cc_final: 0.7480 (mm) REVERT: F 582 ASN cc_start: 0.8720 (m-40) cc_final: 0.8404 (m-40) REVERT: F 661 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.5182 (t80) REVERT: F 746 SER cc_start: 0.8703 (m) cc_final: 0.8419 (p) REVERT: F 821 ILE cc_start: 0.9091 (mt) cc_final: 0.8827 (mt) outliers start: 106 outliers final: 55 residues processed: 506 average time/residue: 0.1887 time to fit residues: 153.7651 Evaluate side-chains 441 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 382 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 299 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 359 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS B 692 GLN C 201 ASN C 748 ASN D 421 GLN D 620 ASN E 309 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 857 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094876 restraints weight = 57827.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096075 restraints weight = 32516.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097193 restraints weight = 21654.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097432 restraints weight = 18413.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097479 restraints weight = 17143.803| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29307 Z= 0.187 Angle : 0.665 14.050 39598 Z= 0.329 Chirality : 0.045 0.217 4479 Planarity : 0.005 0.059 5170 Dihedral : 7.255 86.189 4099 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.42 % Allowed : 13.46 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.73 (0.14), residues: 3563 helix: 0.48 (0.12), residues: 1984 sheet: -2.26 (0.25), residues: 376 loop : -1.38 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 258 TYR 0.022 0.002 TYR D 653 PHE 0.018 0.002 PHE B 729 TRP 0.012 0.002 TRP D 543 HIS 0.005 0.001 HIS D 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (29298) covalent geometry : angle 0.66536 / 0.33 (39598) hydrogen bonds : bond 0.04558 / 3.07 ( 1463) hydrogen bonds : angle 5.02740 / 3.49 ( 4299) Misc. bond : bond 0.00263 / 0.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 408 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7130 (ttpt) REVERT: A 251 TYR cc_start: 0.8285 (m-10) cc_final: 0.7455 (m-10) REVERT: A 293 MET cc_start: 0.4349 (mmm) cc_final: 0.4129 (mmm) REVERT: A 564 GLN cc_start: 0.8588 (tt0) cc_final: 0.8143 (tp-100) REVERT: A 641 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.5863 (p-80) REVERT: A 738 LYS cc_start: 0.7548 (tttt) cc_final: 0.6966 (pttm) REVERT: A 794 HIS cc_start: 0.7548 (m170) cc_final: 0.7294 (t70) REVERT: B 178 ASP cc_start: 0.7902 (m-30) cc_final: 0.7675 (m-30) REVERT: B 581 SER cc_start: 0.9177 (m) cc_final: 0.8938 (p) REVERT: B 708 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: B 808 TYR cc_start: 0.5643 (t80) cc_final: 0.5139 (t80) REVERT: C 241 ASP cc_start: 0.7559 (t0) cc_final: 0.7289 (t0) REVERT: D 163 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8309 (mptt) REVERT: D 827 ASN cc_start: 0.8556 (m-40) cc_final: 0.8068 (m110) REVERT: E 162 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8292 (pttm) REVERT: E 335 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8104 (mtmt) REVERT: E 567 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: E 646 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8961 (pt) REVERT: E 685 ASP cc_start: 0.8542 (t0) cc_final: 0.8316 (t0) REVERT: E 707 VAL cc_start: 0.9558 (t) cc_final: 0.9268 (m) REVERT: E 737 MET cc_start: 0.8764 (tpt) cc_final: 0.8554 (tpp) REVERT: F 540 LEU cc_start: 0.7822 (mm) cc_final: 0.7572 (mm) REVERT: F 582 ASN cc_start: 0.8814 (m-40) cc_final: 0.8463 (m-40) REVERT: F 661 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5100 (t80) REVERT: F 662 LEU cc_start: 0.8666 (tp) cc_final: 0.8427 (mt) REVERT: F 676 LEU cc_start: 0.9367 (tt) cc_final: 0.9013 (tt) REVERT: F 746 SER cc_start: 0.8720 (m) cc_final: 0.8477 (p) REVERT: F 821 ILE cc_start: 0.9101 (mt) cc_final: 0.8831 (mt) outliers start: 103 outliers final: 64 residues processed: 476 average time/residue: 0.1827 time to fit residues: 140.6079 Evaluate side-chains 437 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 368 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 8.9990 chunk 351 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 185 optimal weight: 0.0060 chunk 322 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 339 optimal weight: 0.4980 chunk 191 optimal weight: 4.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.122787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095485 restraints weight = 57806.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097520 restraints weight = 31273.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099175 restraints weight = 20902.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099460 restraints weight = 15749.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099577 restraints weight = 14754.095| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29307 Z= 0.133 Angle : 0.629 16.313 39598 Z= 0.308 Chirality : 0.043 0.237 4479 Planarity : 0.004 0.060 5170 Dihedral : 7.098 83.474 4099 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.09 % Allowed : 14.26 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.49 (0.14), residues: 3563 helix: 0.66 (0.12), residues: 1994 sheet: -2.23 (0.24), residues: 377 loop : -1.22 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 258 TYR 0.024 0.001 TYR B 783 PHE 0.022 0.001 PHE C 729 TRP 0.013 0.001 TRP D 543 HIS 0.007 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (29298) covalent geometry : angle 0.62915 / 0.31 (39598) hydrogen bonds : bond 0.04197 / 2.84 ( 1463) hydrogen bonds : angle 4.87862 / 3.39 ( 4299) Misc. bond : bond 0.00230 / 0.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 422 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7675 (ttpt) cc_final: 0.6989 (ttpt) REVERT: A 251 TYR cc_start: 0.8256 (m-10) cc_final: 0.7443 (m-10) REVERT: A 564 GLN cc_start: 0.8574 (tt0) cc_final: 0.8133 (tp-100) REVERT: A 641 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.5778 (p-80) REVERT: A 738 LYS cc_start: 0.7605 (tttt) cc_final: 0.6939 (pttm) REVERT: B 581 SER cc_start: 0.9148 (m) cc_final: 0.8725 (p) REVERT: B 708 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: B 771 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9012 (mt) REVERT: B 808 TYR cc_start: 0.5535 (t80) cc_final: 0.5177 (t80) REVERT: D 710 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8402 (mtp85) REVERT: D 827 ASN cc_start: 0.8532 (m-40) cc_final: 0.8033 (m110) REVERT: E 162 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8271 (pttm) REVERT: E 567 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7720 (t-90) REVERT: E 685 ASP cc_start: 0.8504 (t0) cc_final: 0.8299 (t0) REVERT: E 707 VAL cc_start: 0.9559 (t) cc_final: 0.9226 (m) REVERT: F 305 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7768 (mtm-85) REVERT: F 403 MET cc_start: 0.8877 (tpt) cc_final: 0.8575 (tpt) REVERT: F 540 LEU cc_start: 0.7790 (mm) cc_final: 0.7546 (mm) REVERT: F 582 ASN cc_start: 0.8833 (m-40) cc_final: 0.8456 (m-40) REVERT: F 661 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.5163 (t80) REVERT: F 676 LEU cc_start: 0.9371 (tt) cc_final: 0.9086 (tt) REVERT: F 737 MET cc_start: 0.8676 (mmm) cc_final: 0.7843 (mtt) REVERT: F 746 SER cc_start: 0.8725 (m) cc_final: 0.8473 (p) REVERT: F 821 ILE cc_start: 0.9083 (mt) cc_final: 0.8817 (mt) outliers start: 93 outliers final: 65 residues processed: 480 average time/residue: 0.1812 time to fit residues: 140.4653 Evaluate side-chains 434 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 293 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 641 HIS C 692 GLN C 748 ASN C 857 GLN E 309 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN F 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092699 restraints weight = 58278.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094778 restraints weight = 32204.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095277 restraints weight = 21929.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096178 restraints weight = 19222.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096468 restraints weight = 15486.788| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29307 Z= 0.218 Angle : 0.696 12.010 39598 Z= 0.343 Chirality : 0.046 0.206 4479 Planarity : 0.005 0.060 5170 Dihedral : 7.208 84.999 4099 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.76 % Allowed : 14.63 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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 (0.14), residues: 3563 helix: 0.69 (0.12), residues: 1990 sheet: -2.31 (0.24), residues: 390 loop : -1.21 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 258 TYR 0.023 0.002 TYR D 653 PHE 0.023 0.002 PHE C 729 TRP 0.019 0.002 TRP E 543 HIS 0.006 0.001 HIS D 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (29298) covalent geometry : angle 0.69574 / 0.34 (39598) hydrogen bonds : bond 0.04640 / 3.12 ( 1463) hydrogen bonds : angle 5.00947 / 3.48 ( 4299) Misc. bond : bond 0.00299 / 0.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 378 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7062 (ttpt) REVERT: A 251 TYR cc_start: 0.8307 (m-10) cc_final: 0.7408 (m-10) REVERT: A 564 GLN cc_start: 0.8571 (tt0) cc_final: 0.8174 (tp-100) REVERT: A 641 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.5836 (p-80) REVERT: A 738 LYS cc_start: 0.7708 (tttt) cc_final: 0.7039 (pttm) REVERT: B 581 SER cc_start: 0.9233 (m) cc_final: 0.8822 (p) REVERT: B 708 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: C 241 ASP cc_start: 0.7855 (t0) cc_final: 0.7540 (t0) REVERT: C 677 ASP cc_start: 0.8146 (t0) cc_final: 0.7760 (t0) REVERT: D 827 ASN cc_start: 0.8547 (m-40) cc_final: 0.8074 (m110) REVERT: E 162 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8322 (pttm) REVERT: E 528 ARG cc_start: 0.6279 (mmt180) cc_final: 0.5842 (mmp80) REVERT: E 567 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: E 707 VAL cc_start: 0.9577 (t) cc_final: 0.9275 (m) REVERT: F 305 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7979 (mtm-85) REVERT: F 582 ASN cc_start: 0.8939 (m-40) cc_final: 0.8469 (m110) REVERT: F 746 SER cc_start: 0.8762 (m) cc_final: 0.8544 (p) REVERT: F 821 ILE cc_start: 0.9077 (mt) cc_final: 0.8797 (mt) REVERT: F 851 ASP cc_start: 0.8158 (t0) cc_final: 0.7785 (t0) outliers start: 113 outliers final: 86 residues processed: 451 average time/residue: 0.1851 time to fit residues: 135.0878 Evaluate side-chains 446 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 357 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 203 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 692 GLN C 195 GLN C 692 GLN C 748 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094221 restraints weight = 58050.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096631 restraints weight = 31806.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098172 restraints weight = 21260.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099126 restraints weight = 16523.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099572 restraints weight = 14198.919| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29307 Z= 0.136 Angle : 0.645 18.715 39598 Z= 0.316 Chirality : 0.044 0.176 4479 Planarity : 0.004 0.059 5170 Dihedral : 7.079 82.282 4099 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 15.62 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.31 (0.14), residues: 3563 helix: 0.81 (0.12), residues: 1995 sheet: -2.25 (0.24), residues: 379 loop : -1.11 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 258 TYR 0.027 0.001 TYR E 319 PHE 0.019 0.002 PHE E 621 TRP 0.015 0.002 TRP E 543 HIS 0.009 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (29298) covalent geometry : angle 0.64454 / 0.32 (39598) hydrogen bonds : bond 0.04219 / 2.85 ( 1463) hydrogen bonds : angle 4.85496 / 3.37 ( 4299) Misc. bond : bond 0.00228 / 0.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 391 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.9128 (mt) cc_final: 0.7636 (mt) REVERT: A 250 LYS cc_start: 0.7677 (ttpt) cc_final: 0.6979 (ttpt) REVERT: A 251 TYR cc_start: 0.8242 (m-10) cc_final: 0.7459 (m-10) REVERT: A 564 GLN cc_start: 0.8546 (tt0) cc_final: 0.8157 (tp-100) REVERT: A 641 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.5731 (p-80) REVERT: A 738 LYS cc_start: 0.7743 (tttt) cc_final: 0.7037 (pttm) REVERT: B 581 SER cc_start: 0.9192 (m) cc_final: 0.8765 (p) REVERT: B 708 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: C 633 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8097 (t0) REVERT: C 677 ASP cc_start: 0.8133 (t0) cc_final: 0.7779 (t0) REVERT: C 708 ASP cc_start: 0.7943 (t0) cc_final: 0.7698 (t0) REVERT: C 747 HIS cc_start: 0.7159 (t-90) cc_final: 0.6885 (t70) REVERT: D 827 ASN cc_start: 0.8492 (m-40) cc_final: 0.8024 (m110) REVERT: E 162 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8297 (pttm) REVERT: E 528 ARG cc_start: 0.6226 (mmt180) cc_final: 0.5688 (mmp80) REVERT: E 567 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (t-90) REVERT: E 581 SER cc_start: 0.9250 (m) cc_final: 0.8962 (p) REVERT: E 707 VAL cc_start: 0.9573 (t) cc_final: 0.9252 (m) REVERT: E 737 MET cc_start: 0.8869 (tpt) cc_final: 0.8279 (tpp) REVERT: F 191 ILE cc_start: 0.8505 (pt) cc_final: 0.8184 (tt) REVERT: F 403 MET cc_start: 0.8741 (tpt) cc_final: 0.8530 (tpp) REVERT: F 582 ASN cc_start: 0.8878 (m-40) cc_final: 0.8405 (m110) REVERT: F 737 MET cc_start: 0.8655 (mmm) cc_final: 0.7916 (mtt) REVERT: F 746 SER cc_start: 0.8710 (m) cc_final: 0.8462 (p) REVERT: F 821 ILE cc_start: 0.9089 (mt) cc_final: 0.8823 (mt) outliers start: 87 outliers final: 68 residues processed: 448 average time/residue: 0.1847 time to fit residues: 133.7625 Evaluate side-chains 431 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 359 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 231 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 6 optimal weight: 0.0370 chunk 294 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 291 optimal weight: 0.0270 chunk 62 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN C 692 GLN ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093709 restraints weight = 58199.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096135 restraints weight = 31940.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097699 restraints weight = 21403.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098683 restraints weight = 16624.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099125 restraints weight = 14260.355| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29307 Z= 0.145 Angle : 0.658 19.282 39598 Z= 0.321 Chirality : 0.044 0.246 4479 Planarity : 0.004 0.059 5170 Dihedral : 7.029 80.516 4099 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.86 % Allowed : 16.09 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.23 (0.14), residues: 3563 helix: 0.86 (0.12), residues: 1994 sheet: -2.20 (0.24), residues: 379 loop : -1.05 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 815 TYR 0.027 0.001 TYR B 783 PHE 0.026 0.002 PHE C 729 TRP 0.016 0.002 TRP E 543 HIS 0.004 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (29298) covalent geometry : angle 0.65762 / 0.32 (39598) hydrogen bonds : bond 0.04185 / 2.82 ( 1463) hydrogen bonds : angle 4.84178 / 3.36 ( 4299) Misc. bond : bond 0.00210 / 0.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 382 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7011 (ttpt) REVERT: A 251 TYR cc_start: 0.8234 (m-10) cc_final: 0.7422 (m-10) REVERT: A 564 GLN cc_start: 0.8564 (tt0) cc_final: 0.8155 (tp-100) REVERT: A 641 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.5736 (p-80) REVERT: A 738 LYS cc_start: 0.7747 (tttt) cc_final: 0.7046 (pttm) REVERT: A 823 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7623 (mm-40) REVERT: B 581 SER cc_start: 0.9214 (m) cc_final: 0.8777 (p) REVERT: B 708 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: B 783 TYR cc_start: 0.7389 (m-10) cc_final: 0.7150 (m-80) REVERT: C 633 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8208 (t0) REVERT: C 677 ASP cc_start: 0.8152 (t0) cc_final: 0.7831 (t0) REVERT: C 708 ASP cc_start: 0.7983 (t0) cc_final: 0.7716 (t0) REVERT: D 189 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8413 (ttt-90) REVERT: D 305 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7791 (ttp-110) REVERT: D 551 MET cc_start: 0.6933 (mmm) cc_final: 0.6701 (mmm) REVERT: D 827 ASN cc_start: 0.8507 (m-40) cc_final: 0.7959 (m110) REVERT: E 162 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8299 (pttm) REVERT: E 528 ARG cc_start: 0.6129 (mmt180) cc_final: 0.5555 (mmp80) REVERT: E 581 SER cc_start: 0.9248 (m) cc_final: 0.8951 (p) REVERT: E 685 ASP cc_start: 0.8553 (t0) cc_final: 0.8352 (t0) REVERT: E 707 VAL cc_start: 0.9570 (t) cc_final: 0.9237 (m) REVERT: E 737 MET cc_start: 0.8845 (tpt) cc_final: 0.8261 (tpp) REVERT: E 756 ARG cc_start: 0.7954 (mmt90) cc_final: 0.7673 (tpp80) REVERT: F 403 MET cc_start: 0.8735 (tpt) cc_final: 0.8530 (tpp) REVERT: F 582 ASN cc_start: 0.8904 (m-40) cc_final: 0.8422 (m110) REVERT: F 622 MET cc_start: 0.7440 (mtm) cc_final: 0.7182 (mtm) REVERT: F 737 MET cc_start: 0.8694 (mmm) cc_final: 0.7964 (mtt) REVERT: F 746 SER cc_start: 0.8648 (m) cc_final: 0.8383 (p) REVERT: F 821 ILE cc_start: 0.9091 (mt) cc_final: 0.8822 (mt) outliers start: 86 outliers final: 71 residues processed: 439 average time/residue: 0.1847 time to fit residues: 131.5958 Evaluate side-chains 435 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9990 chunk 190 optimal weight: 0.0980 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 353 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 320 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 692 GLN C 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 567 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094204 restraints weight = 57934.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096694 restraints weight = 31077.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098313 restraints weight = 20582.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099327 restraints weight = 15842.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099792 restraints weight = 13555.071| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29307 Z= 0.132 Angle : 0.662 20.303 39598 Z= 0.320 Chirality : 0.044 0.250 4479 Planarity : 0.004 0.059 5170 Dihedral : 6.969 78.535 4099 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.59 % Allowed : 16.39 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.11 (0.14), residues: 3563 helix: 0.96 (0.12), residues: 1976 sheet: -2.18 (0.24), residues: 380 loop : -0.97 (0.19), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 258 TYR 0.025 0.001 TYR E 319 PHE 0.023 0.001 PHE B 729 TRP 0.017 0.002 TRP E 543 HIS 0.004 0.001 HIS D 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29298) covalent geometry : angle 0.66191 / 0.32 (39598) hydrogen bonds : bond 0.04073 / 2.76 ( 1463) hydrogen bonds : angle 4.79642 / 3.33 ( 4299) Misc. bond : bond 0.00204 / 0.09 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7022 (ttpt) REVERT: A 251 TYR cc_start: 0.8217 (m-10) cc_final: 0.7415 (m-10) REVERT: A 564 GLN cc_start: 0.8535 (tt0) cc_final: 0.8137 (tp-100) REVERT: A 641 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5754 (p-80) REVERT: A 738 LYS cc_start: 0.7769 (tttt) cc_final: 0.7050 (pttm) REVERT: A 823 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7601 (mm-40) REVERT: B 242 MET cc_start: 0.7527 (ttm) cc_final: 0.7248 (tpp) REVERT: B 581 SER cc_start: 0.9208 (m) cc_final: 0.8813 (p) REVERT: B 708 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: C 633 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8344 (t0) REVERT: C 677 ASP cc_start: 0.8209 (t0) cc_final: 0.7917 (t0) REVERT: C 708 ASP cc_start: 0.7993 (t0) cc_final: 0.7715 (t0) REVERT: C 742 LEU cc_start: 0.9357 (tp) cc_final: 0.9108 (tt) REVERT: C 757 ILE cc_start: 0.9559 (mm) cc_final: 0.9292 (mt) REVERT: C 802 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8953 (tp) REVERT: D 827 ASN cc_start: 0.8496 (m-40) cc_final: 0.7944 (m110) REVERT: E 162 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8282 (pttm) REVERT: E 528 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5597 (mmp80) REVERT: E 581 SER cc_start: 0.9233 (m) cc_final: 0.8898 (p) REVERT: E 636 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7098 (mt-10) REVERT: E 707 VAL cc_start: 0.9549 (t) cc_final: 0.9211 (m) REVERT: E 756 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7624 (tpp80) REVERT: F 217 GLU cc_start: 0.8448 (pt0) cc_final: 0.7447 (tm-30) REVERT: F 403 MET cc_start: 0.8716 (tpt) cc_final: 0.8503 (tpp) REVERT: F 582 ASN cc_start: 0.8863 (m-40) cc_final: 0.8381 (m110) REVERT: F 622 MET cc_start: 0.7396 (mtm) cc_final: 0.7148 (mtm) REVERT: F 737 MET cc_start: 0.8676 (mmm) cc_final: 0.7983 (mtt) REVERT: F 746 SER cc_start: 0.8609 (m) cc_final: 0.8341 (p) REVERT: F 821 ILE cc_start: 0.9075 (mt) cc_final: 0.8807 (mt) outliers start: 78 outliers final: 68 residues processed: 432 average time/residue: 0.1850 time to fit residues: 130.0565 Evaluate side-chains 428 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 356 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 339 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS B 692 GLN C 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 567 HIS ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094310 restraints weight = 58533.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095913 restraints weight = 31903.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097760 restraints weight = 20245.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097921 restraints weight = 16637.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097782 restraints weight = 15029.551| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29307 Z= 0.182 Angle : 0.689 20.398 39598 Z= 0.336 Chirality : 0.045 0.239 4479 Planarity : 0.005 0.064 5170 Dihedral : 7.028 79.305 4099 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.79 % Allowed : 16.42 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.13 (0.14), residues: 3563 helix: 0.94 (0.12), residues: 1986 sheet: -2.24 (0.24), residues: 381 loop : -0.94 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 258 TYR 0.024 0.001 TYR E 319 PHE 0.037 0.002 PHE D 276 TRP 0.028 0.002 TRP E 543 HIS 0.006 0.001 HIS D 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (29298) covalent geometry : angle 0.68912 / 0.34 (39598) hydrogen bonds : bond 0.04297 / 2.90 ( 1463) hydrogen bonds : angle 4.86087 / 3.37 ( 4299) Misc. bond : bond 0.00239 / 0.11 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.66 seconds wall clock time: 89 minutes 10.70 seconds (5350.70 seconds total)