Starting phenix.real_space_refine on Mon Sep 14 20:05:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rn3_4941/09_2026/6rn3_4941.cif" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 127 5.16 5 C 20485 2.51 5 N 5933 2.21 5 O 6295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 32871 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 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: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 664} 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: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} 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: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 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: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 659} 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: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 651} Chain breaks: 5 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: "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: 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} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.19 Number of scatterers: 32871 At special positions: 0 Unit cell: (144.56, 182, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 P 31 15.00 O 6295 8.00 N 5933 7.00 C 20485 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=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 29 sheets defined 63.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.639A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 254 through 270 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 295 through 305 Proline residue: A 301 - end of helix removed outlier: 3.727A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.877A pdb=" N PHE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.509A pdb=" N ILE A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 removed outlier: 4.222A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 443 through 493 Processing helix chain 'A' and resid 494 through 524 removed outlier: 3.849A pdb=" N MET A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.604A pdb=" N ILE A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.570A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.559A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.522A 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: 3.869A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.785A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.713A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 4.307A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.545A pdb=" N ILE B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 406 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 443 through 493 Processing helix chain 'B' and resid 494 through 524 removed outlier: 3.958A pdb=" N MET B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 532 through 545 removed outlier: 3.670A pdb=" N GLY B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 570 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.532A pdb=" N GLY B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 removed outlier: 3.590A pdb=" N CYS B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 648 Processing helix chain 'B' and resid 653 through 659 removed outlier: 3.692A pdb=" N TYR B 656 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 659 " --> pdb=" O TYR B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 653 through 659' Processing helix chain 'B' and resid 661 through 669 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.687A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 805 Processing helix chain 'B' and resid 814 through 835 Proline residue: B 828 - end of helix 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 removed outlier: 3.607A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.648A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.602A pdb=" N LEU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.869A pdb=" N MET C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 284' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.564A pdb=" N HIS C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.564A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.752A pdb=" N ILE C 391 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 443 through 493 Processing helix chain 'C' and resid 494 through 524 removed outlier: 4.014A pdb=" N MET C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 532 through 544 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 removed outlier: 3.765A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 640 through 647 Processing helix chain 'C' and resid 661 through 669 removed outlier: 4.250A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 removed outlier: 3.746A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.833A pdb=" N PHE C 687 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 4.078A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 removed outlier: 3.515A pdb=" N MET C 737 " --> pdb=" O ASP C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 790 Processing helix chain 'C' and resid 796 through 806 Processing helix chain 'C' and resid 814 through 834 Proline residue: C 828 - end of helix removed outlier: 3.552A pdb=" N LEU C 834 " --> pdb=" O ALA C 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.505A pdb=" N GLN D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 248 removed outlier: 3.889A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.761A pdb=" N MET D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.611A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.592A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 342 through 361 Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.620A pdb=" N ILE D 391 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 443 through 493 Processing helix chain 'D' and resid 494 through 524 removed outlier: 3.950A pdb=" N MET D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.851A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.528A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.618A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'D' and resid 639 through 643 Processing helix chain 'D' and resid 655 through 659 removed outlier: 4.129A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.636A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 697 removed outlier: 4.365A 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 Processing helix chain 'D' and resid 750 through 757 removed outlier: 3.515A pdb=" N ARG D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 757 " --> pdb=" O PHE D 753 " (cutoff:3.500A) 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 825 removed outlier: 3.875A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 834 Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.544A pdb=" N LYS E 162 " --> pdb=" O GLN E 159 " (cutoff:3.500A) 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 226 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 242 through 247 removed outlier: 3.708A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 Processing helix chain 'E' and resid 279 through 285 removed outlier: 4.465A pdb=" N GLY E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.667A pdb=" N LEU E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 299 through 304' Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.779A pdb=" N LEU E 329 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 366 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 3.627A pdb=" N ILE E 391 " --> pdb=" O PRO E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 430 Processing helix chain 'E' and resid 443 through 493 Processing helix chain 'E' and resid 495 through 524 removed outlier: 3.691A pdb=" N SER E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 532 through 542 removed outlier: 3.615A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 561 removed outlier: 3.890A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG E 561 " --> pdb=" O GLU E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 568 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.763A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 623 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 653 through 657 removed outlier: 3.939A pdb=" N TYR E 656 " --> pdb=" O TYR E 653 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 657 " --> pdb=" O VAL E 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 653 through 657' Processing helix chain 'E' and resid 661 through 666 removed outlier: 3.532A pdb=" N ALA E 665 " --> pdb=" O TYR E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.546A pdb=" N LYS E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 696 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 734 through 749 Processing helix chain 'E' and resid 750 through 755 Processing helix chain 'E' and resid 767 through 790 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 814 through 835 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 Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 253 through 269 Processing helix chain 'F' and resid 279 through 285 removed outlier: 3.910A pdb=" N MET F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.926A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 4.241A pdb=" N LEU F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS F 360 " --> pdb=" O ARG F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' Processing helix chain 'F' and resid 366 through 380 Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 443 through 493 Processing helix chain 'F' and resid 494 through 524 removed outlier: 3.794A pdb=" N MET F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 569 Processing helix chain 'F' and resid 573 through 588 Processing helix chain 'F' and resid 610 through 623 Processing helix chain 'F' and resid 662 through 669 removed outlier: 3.726A pdb=" N VAL F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.664A pdb=" N LYS F 681 " --> pdb=" O ALA F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 696 Processing helix chain 'F' and resid 720 through 729 Processing helix chain 'F' and resid 734 through 749 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 834 Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 6.472A pdb=" N ARG A 236 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 276 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 314 removed outlier: 8.303A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 365 removed outlier: 7.595A pdb=" N GLN A 364 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 633 removed outlier: 6.167A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 600 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 792 through 795 removed outlier: 6.851A pdb=" N GLU A 792 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 846 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS A 794 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL A 848 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.951A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.049A 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: 7.160A 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 631 removed outlier: 6.349A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 714 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER B 600 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 761 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 602 " --> pdb=" O VAL B 761 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB1, first strand: chain 'B' and resid 792 through 795 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.590A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.697A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.514A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY C 599 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET C 716 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 761 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 602 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 793 through 795 Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.167A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 203 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 364 through 365 removed outlier: 7.068A 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 602 through 603 removed outlier: 6.625A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.599A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.775A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 240 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL E 311 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU E 275 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA E 313 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE E 277 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N THR E 315 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 206 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 201 through 202 removed outlier: 7.583A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.508A 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 601 through 603 Processing sheet with id=AC5, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.619A pdb=" N VAL E 707 " --> pdb=" O LEU E 699 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 793 through 795 removed outlier: 7.418A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.951A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 312 through 314 Processing sheet with id=AC9, first strand: chain 'F' and resid 629 through 633 removed outlier: 3.702A pdb=" N THR F 717 " --> pdb=" O LEU F 676 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER F 600 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL F 761 " --> pdb=" O SER F 600 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (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: 6.929A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1827 hydrogen bonds defined for protein. 5391 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: 6.94 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11712 1.36 - 1.51: 9837 1.51 - 1.66: 11539 1.66 - 1.80: 211 1.80 - 1.95: 22 Bond restraints: 33321 Sorted by residual: bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.528 1.427 0.101 2.61e-02 1.47e+03 1.51e+01 bond pdb=" C ALA E 814 " pdb=" N ARG E 815 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.09e-02 8.42e+03 9.48e+00 bond pdb=" CG ARG E 815 " pdb=" CD ARG E 815 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.81e+00 bond pdb=" CA SER D 600 " pdb=" CB SER D 600 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" CA ALA B 628 " pdb=" CB ALA B 628 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.51e-02 4.39e+03 7.23e+00 ... (remaining 33316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 44478 4.20 - 8.41: 452 8.41 - 12.61: 33 12.61 - 16.82: 3 16.82 - 21.02: 4 Bond angle restraints: 44970 Sorted by residual: angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CA PRO B 409 " ideal model delta sigma weight residual 127.00 148.02 -21.02 2.40e+00 1.74e-01 7.67e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CA PRO E 409 " ideal model delta sigma weight residual 127.00 147.50 -20.50 2.40e+00 1.74e-01 7.30e+01 angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 120.60 103.18 17.42 2.20e+00 2.07e-01 6.27e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CD PRO E 409 " ideal model delta sigma weight residual 120.60 103.33 17.27 2.20e+00 2.07e-01 6.16e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 113.50 106.47 7.03 1.23e+00 6.61e-01 3.26e+01 ... (remaining 44965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 20108 26.42 - 52.85: 412 52.85 - 79.27: 33 79.27 - 105.70: 5 105.70 - 132.12: 2 Dihedral angle restraints: 20560 sinusoidal: 8676 harmonic: 11884 Sorted by residual: dihedral pdb=" CA GLU C 207 " pdb=" C GLU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA HIS E 568 " pdb=" C HIS E 568 " pdb=" N ARG E 569 " pdb=" CA ARG E 569 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA LEU F 245 " pdb=" C LEU F 245 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " ideal model delta harmonic sigma weight residual -180.00 -147.73 -32.27 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 20557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3464 0.057 - 0.114: 1286 0.114 - 0.172: 294 0.172 - 0.229: 41 0.229 - 0.286: 8 Chirality restraints: 5093 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 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG D 815 " pdb=" N ARG D 815 " pdb=" C ARG D 815 " pdb=" CB ARG D 815 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5090 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.056 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.026 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 301 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 683 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 684 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " 0.043 5.00e-02 4.00e+02 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3689 2.74 - 3.28: 31586 3.28 - 3.82: 53987 3.82 - 4.36: 63138 4.36 - 4.90: 107130 Nonbonded interactions: 259530 Sorted by model distance: nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.198 3.040 nonbonded pdb=" O1B AGS E1002 " pdb=" O2A AGS E1002 " model vdw 2.199 3.040 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.220 3.040 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.232 3.040 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.235 3.040 ... (remaining 259525 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 543 or resid 553 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 543 or resid 553 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'F' and resid 159 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.010 0.109 33340 Z= 0.453 Angle : 1.151 21.024 44970 Z= 0.615 Chirality : 0.061 0.286 5093 Planarity : 0.008 0.086 5872 Dihedral : 10.838 132.121 12880 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 0.35 % Allowed : 0.90 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % 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: -3.79 (0.11), residues: 4053 helix: -2.10 (0.08), residues: 2310 sheet: -3.11 (0.23), residues: 374 loop : -2.76 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 815 TYR 0.028 0.003 TYR F 671 PHE 0.046 0.004 PHE C 763 TRP 0.037 0.005 TRP D 543 HIS 0.018 0.003 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.01050 / 0.45 (33321) covalent geometry : angle 1.15069 / 0.61 (44970) hydrogen bonds : bond 0.14656 / 10.15 ( 1827) hydrogen bonds : angle 7.22084 / 5.09 ( 5391) Misc. bond : bond 0.00612 / 0.38 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1138 time to evaluate : 1.067 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7701 (mtpp) REVERT: A 180 VAL cc_start: 0.6759 (t) cc_final: 0.6313 (m) REVERT: A 181 ILE cc_start: 0.8080 (mt) cc_final: 0.7876 (mp) REVERT: A 241 ASP cc_start: 0.7032 (t0) cc_final: 0.6748 (t0) REVERT: A 322 TYR cc_start: 0.8094 (m-80) cc_final: 0.7884 (m-80) REVERT: A 363 VAL cc_start: 0.6968 (m) cc_final: 0.6191 (m) REVERT: A 430 MET cc_start: -0.1309 (mmm) cc_final: -0.1609 (mtm) REVERT: A 616 LYS cc_start: 0.7333 (mttt) cc_final: 0.7001 (mttt) REVERT: A 740 LEU cc_start: 0.7619 (tp) cc_final: 0.7307 (pp) REVERT: A 804 SER cc_start: 0.5371 (t) cc_final: 0.5079 (p) REVERT: B 194 LEU cc_start: 0.8817 (mt) cc_final: 0.8567 (mp) REVERT: B 457 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8460 (tm-30) REVERT: B 524 MET cc_start: 0.1090 (mmm) cc_final: -0.0488 (ptt) REVERT: B 533 ASP cc_start: 0.8393 (p0) cc_final: 0.8108 (p0) REVERT: B 562 MET cc_start: 0.6919 (tmt) cc_final: 0.5970 (ttp) REVERT: B 633 ASP cc_start: 0.8186 (m-30) cc_final: 0.7353 (m-30) REVERT: B 634 MET cc_start: 0.7932 (mmm) cc_final: 0.7460 (tpp) REVERT: B 685 ASP cc_start: 0.7333 (p0) cc_final: 0.6810 (p0) REVERT: B 693 VAL cc_start: 0.8838 (t) cc_final: 0.8613 (t) REVERT: B 736 HIS cc_start: 0.8142 (m170) cc_final: 0.7702 (m90) REVERT: B 747 HIS cc_start: 0.7110 (m-70) cc_final: 0.6820 (m90) REVERT: B 802 LEU cc_start: 0.8343 (mp) cc_final: 0.8086 (pp) REVERT: C 178 ASP cc_start: 0.7721 (m-30) cc_final: 0.7419 (p0) REVERT: C 200 ASN cc_start: 0.8927 (m-40) cc_final: 0.7958 (p0) REVERT: C 217 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 259 LEU cc_start: 0.7925 (tp) cc_final: 0.6721 (tp) REVERT: C 314 THR cc_start: 0.8978 (t) cc_final: 0.8731 (p) REVERT: C 345 ASP cc_start: 0.8007 (m-30) cc_final: 0.7222 (t0) REVERT: C 410 GLU cc_start: 0.3172 (mp0) cc_final: 0.2575 (tt0) REVERT: C 656 TYR cc_start: 0.7566 (t80) cc_final: 0.7024 (t80) REVERT: C 696 ASP cc_start: 0.7786 (m-30) cc_final: 0.7473 (m-30) REVERT: C 747 HIS cc_start: 0.8027 (m-70) cc_final: 0.7811 (m-70) REVERT: C 791 TYR cc_start: 0.7319 (m-80) cc_final: 0.6325 (m-10) REVERT: D 187 ILE cc_start: 0.7700 (mt) cc_final: 0.7492 (mt) REVERT: D 293 MET cc_start: 0.3836 (tpt) cc_final: 0.3545 (tpp) REVERT: D 319 TYR cc_start: 0.8737 (t80) cc_final: 0.8159 (t80) REVERT: D 430 MET cc_start: 0.2930 (mmm) cc_final: 0.1866 (ppp) REVERT: D 562 MET cc_start: 0.8153 (tpt) cc_final: 0.7909 (tpt) REVERT: D 630 VAL cc_start: 0.8412 (t) cc_final: 0.8143 (t) REVERT: D 680 GLU cc_start: 0.8065 (pm20) cc_final: 0.7437 (pp20) REVERT: D 689 ILE cc_start: 0.8038 (mm) cc_final: 0.7291 (mm) REVERT: D 780 LYS cc_start: 0.8726 (mttt) cc_final: 0.8205 (tmmt) REVERT: D 808 TYR cc_start: 0.6799 (t80) cc_final: 0.6405 (t80) REVERT: D 827 ASN cc_start: 0.8791 (m-40) cc_final: 0.8484 (m110) REVERT: E 185 GLU cc_start: 0.8328 (tt0) cc_final: 0.7955 (tp30) REVERT: E 187 ILE cc_start: 0.7993 (mt) cc_final: 0.7789 (mt) REVERT: E 460 GLU cc_start: 0.8667 (tp30) cc_final: 0.8303 (mm-30) REVERT: E 551 MET cc_start: 0.6682 (mmp) cc_final: 0.6310 (mtm) REVERT: E 739 GLU cc_start: 0.8263 (tp30) cc_final: 0.7685 (pt0) REVERT: E 762 VAL cc_start: 0.7432 (t) cc_final: 0.7146 (p) REVERT: E 783 TYR cc_start: 0.7344 (m-10) cc_final: 0.6912 (m-10) REVERT: E 784 LYS cc_start: 0.9032 (tttt) cc_final: 0.8829 (ptpt) REVERT: F 245 LEU cc_start: 0.8758 (mt) cc_final: 0.8228 (mp) REVERT: F 582 ASN cc_start: 0.8539 (m-40) cc_final: 0.8225 (t0) REVERT: F 673 VAL cc_start: 0.7253 (t) cc_final: 0.6958 (m) REVERT: F 680 GLU cc_start: 0.6386 (pm20) cc_final: 0.6160 (pm20) REVERT: F 686 VAL cc_start: 0.7984 (t) cc_final: 0.7478 (t) REVERT: F 766 LEU cc_start: 0.7586 (pt) cc_final: 0.6738 (mp) REVERT: F 779 LEU cc_start: 0.7997 (mm) cc_final: 0.7553 (tp) REVERT: F 795 ILE cc_start: 0.7435 (tt) cc_final: 0.7152 (tt) REVERT: F 796 SER cc_start: 0.8671 (t) cc_final: 0.8328 (p) REVERT: F 817 LEU cc_start: 0.8942 (tp) cc_final: 0.8533 (tp) REVERT: F 821 ILE cc_start: 0.8586 (mt) cc_final: 0.8104 (mt) outliers start: 12 outliers final: 0 residues processed: 1149 average time/residue: 0.2289 time to fit residues: 406.8023 Evaluate side-chains 609 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 361 HIS A 726 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS B 281 HIS B 334 GLN B 362 HIS B 620 ASN B 641 HIS B 748 ASN B 794 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 264 ASN C 512 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN D 195 GLN D 281 HIS D 567 HIS D 595 ASN D 692 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D 858 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS E 309 HIS E 427 GLN E 512 GLN E 567 HIS E 755 ASN E 806 ASN E 857 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 361 HIS F 512 GLN F 688 ASN F 747 HIS F 770 HIS F 831 GLN F 849 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108303 restraints weight = 67983.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109497 restraints weight = 45483.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109978 restraints weight = 28887.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110852 restraints weight = 25903.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110922 restraints weight = 21791.578| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33340 Z= 0.168 Angle : 0.737 9.815 44970 Z= 0.379 Chirality : 0.045 0.262 5093 Planarity : 0.006 0.070 5872 Dihedral : 8.599 128.380 4642 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.79 % Allowed : 11.47 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.96 (0.12), residues: 4053 helix: -0.46 (0.10), residues: 2341 sheet: -2.74 (0.24), residues: 377 loop : -2.18 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 756 TYR 0.025 0.002 TYR F 671 PHE 0.017 0.002 PHE B 729 TRP 0.019 0.003 TRP C 543 HIS 0.020 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (33321) covalent geometry : angle 0.73727 / 0.38 (44970) hydrogen bonds : bond 0.05133 / 3.49 ( 1827) hydrogen bonds : angle 5.44467 / 3.81 ( 5391) Misc. bond : bond 0.00283 / 0.15 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 700 time to evaluate : 1.220 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 242 MET cc_start: 0.7983 (mmt) cc_final: 0.7586 (mmt) REVERT: A 298 MET cc_start: 0.7677 (mmm) cc_final: 0.7417 (tpt) REVERT: A 322 TYR cc_start: 0.8111 (m-80) cc_final: 0.7898 (m-80) REVERT: A 481 GLN cc_start: 0.6562 (pt0) cc_final: 0.5928 (tt0) REVERT: A 519 LEU cc_start: 0.8124 (tp) cc_final: 0.7863 (mp) REVERT: A 623 PHE cc_start: 0.6955 (t80) cc_final: 0.6622 (t80) REVERT: B 335 LYS cc_start: 0.7389 (mtpt) cc_final: 0.7182 (tttt) REVERT: B 358 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6763 (pt0) REVERT: B 524 MET cc_start: 0.1381 (mmm) cc_final: -0.0279 (ptt) REVERT: B 533 ASP cc_start: 0.8012 (p0) cc_final: 0.7748 (p0) REVERT: B 584 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8975 (tp) REVERT: B 633 ASP cc_start: 0.7778 (m-30) cc_final: 0.6675 (m-30) REVERT: B 634 MET cc_start: 0.7707 (mmm) cc_final: 0.7336 (tpp) REVERT: B 685 ASP cc_start: 0.6992 (p0) cc_final: 0.6719 (p0) REVERT: B 758 ASP cc_start: 0.8150 (t0) cc_final: 0.7918 (t0) REVERT: C 345 ASP cc_start: 0.7584 (m-30) cc_final: 0.7054 (t0) REVERT: C 405 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (mt) REVERT: C 524 MET cc_start: 0.5048 (tpp) cc_final: 0.4488 (tpt) REVERT: C 656 TYR cc_start: 0.7609 (t80) cc_final: 0.7298 (t80) REVERT: C 696 ASP cc_start: 0.7998 (m-30) cc_final: 0.7578 (m-30) REVERT: C 700 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7555 (p) REVERT: D 252 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6026 (ttt180) REVERT: D 317 ASP cc_start: 0.8425 (t0) cc_final: 0.8138 (t0) REVERT: D 319 TYR cc_start: 0.8406 (t80) cc_final: 0.8016 (t80) REVERT: D 430 MET cc_start: 0.3099 (mmm) cc_final: 0.2196 (ppp) REVERT: D 533 ASP cc_start: 0.7336 (p0) cc_final: 0.6886 (m-30) REVERT: D 552 MET cc_start: 0.7414 (ppp) cc_final: 0.7008 (ppp) REVERT: D 614 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9097 (tt) REVERT: D 642 SER cc_start: 0.8885 (m) cc_final: 0.8548 (t) REVERT: D 692 GLN cc_start: 0.7528 (tt0) cc_final: 0.7141 (tt0) REVERT: D 780 LYS cc_start: 0.8607 (mttt) cc_final: 0.8375 (tmmt) REVERT: D 797 ASP cc_start: 0.7756 (p0) cc_final: 0.7521 (p0) REVERT: D 827 ASN cc_start: 0.8554 (m-40) cc_final: 0.7282 (m110) REVERT: E 526 LEU cc_start: 0.6690 (mt) cc_final: 0.6325 (tt) REVERT: E 633 ASP cc_start: 0.5890 (t0) cc_final: 0.5640 (m-30) REVERT: E 683 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6599 (m170) REVERT: E 737 MET cc_start: 0.7065 (tpp) cc_final: 0.6670 (tpp) REVERT: E 783 TYR cc_start: 0.7311 (m-10) cc_final: 0.7065 (m-10) REVERT: E 821 ILE cc_start: 0.8490 (mt) cc_final: 0.8225 (mp) REVERT: F 282 THR cc_start: 0.7734 (m) cc_final: 0.7029 (m) REVERT: F 336 VAL cc_start: 0.8717 (t) cc_final: 0.8502 (m) REVERT: F 582 ASN cc_start: 0.8425 (m-40) cc_final: 0.8042 (t0) REVERT: F 766 LEU cc_start: 0.7123 (pt) cc_final: 0.6588 (mp) REVERT: F 817 LEU cc_start: 0.9052 (tp) cc_final: 0.8578 (tp) REVERT: F 821 ILE cc_start: 0.8257 (mt) cc_final: 0.7823 (mt) REVERT: F 850 GLU cc_start: 0.5743 (pm20) cc_final: 0.5393 (tt0) outliers start: 96 outliers final: 43 residues processed: 763 average time/residue: 0.2004 time to fit residues: 250.6479 Evaluate side-chains 602 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 553 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 264 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 281 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 154 optimal weight: 0.0970 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 512 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 823 GLN F 269 GLN F 849 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104383 restraints weight = 68856.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105617 restraints weight = 41775.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106593 restraints weight = 30557.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107375 restraints weight = 25036.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107547 restraints weight = 21246.427| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 33340 Z= 0.217 Angle : 0.769 24.398 44970 Z= 0.392 Chirality : 0.046 0.295 5093 Planarity : 0.005 0.064 5872 Dihedral : 8.359 160.972 4642 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.17 % Allowed : 13.91 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.23 (0.13), residues: 4053 helix: 0.23 (0.10), residues: 2339 sheet: -2.58 (0.24), residues: 421 loop : -1.98 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 815 TYR 0.037 0.002 TYR B 783 PHE 0.021 0.003 PHE F 621 TRP 0.018 0.003 TRP D 462 HIS 0.010 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (33321) covalent geometry : angle 0.76912 / 0.39 (44970) hydrogen bonds : bond 0.04960 / 3.36 ( 1827) hydrogen bonds : angle 5.18038 / 3.64 ( 5391) Misc. bond : bond 0.00508 / 0.25 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 580 time to evaluate : 1.094 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 242 MET cc_start: 0.8230 (mmt) cc_final: 0.7988 (mmt) REVERT: A 481 GLN cc_start: 0.6586 (pt0) cc_final: 0.5880 (tt0) REVERT: A 519 LEU cc_start: 0.7957 (tp) cc_final: 0.7735 (mt) REVERT: B 358 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7201 (pt0) REVERT: B 533 ASP cc_start: 0.8062 (p0) cc_final: 0.7798 (p0) REVERT: B 634 MET cc_start: 0.7896 (mmm) cc_final: 0.7675 (tpp) REVERT: B 685 ASP cc_start: 0.7147 (p0) cc_final: 0.6935 (p0) REVERT: B 783 TYR cc_start: 0.7884 (m-80) cc_final: 0.7505 (m-80) REVERT: C 260 LYS cc_start: 0.8924 (tttt) cc_final: 0.8636 (tptt) REVERT: C 280 LEU cc_start: 0.9195 (tp) cc_final: 0.8821 (tp) REVERT: C 293 MET cc_start: 0.7812 (tpp) cc_final: 0.7134 (tmm) REVERT: C 345 ASP cc_start: 0.7371 (m-30) cc_final: 0.6859 (t0) REVERT: C 385 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8072 (mm-40) REVERT: C 696 ASP cc_start: 0.8217 (m-30) cc_final: 0.7760 (m-30) REVERT: C 759 GLU cc_start: 0.6976 (mp0) cc_final: 0.6768 (mp0) REVERT: D 252 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6208 (ttp-170) REVERT: D 430 MET cc_start: 0.2571 (mmm) cc_final: 0.1902 (ppp) REVERT: D 601 PHE cc_start: 0.7731 (m-80) cc_final: 0.7529 (m-80) REVERT: D 614 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9380 (tt) REVERT: D 642 SER cc_start: 0.9045 (m) cc_final: 0.8836 (t) REVERT: D 677 ASP cc_start: 0.7566 (t0) cc_final: 0.7345 (t0) REVERT: D 692 GLN cc_start: 0.7727 (tt0) cc_final: 0.7427 (tt0) REVERT: D 752 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7135 (mt-10) REVERT: D 797 ASP cc_start: 0.7932 (p0) cc_final: 0.7640 (p0) REVERT: D 822 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7263 (tp40) REVERT: D 827 ASN cc_start: 0.8453 (m-40) cc_final: 0.8237 (m110) REVERT: E 319 TYR cc_start: 0.8308 (t80) cc_final: 0.8049 (t80) REVERT: E 330 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7107 (tp30) REVERT: E 460 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7962 (tp30) REVERT: E 614 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9063 (tt) REVERT: E 618 LEU cc_start: 0.9056 (mt) cc_final: 0.8795 (tp) REVERT: E 633 ASP cc_start: 0.6989 (t0) cc_final: 0.6658 (m-30) REVERT: E 737 MET cc_start: 0.7336 (tpp) cc_final: 0.7070 (tpp) REVERT: E 783 TYR cc_start: 0.7522 (m-10) cc_final: 0.7246 (m-10) REVERT: F 336 VAL cc_start: 0.8789 (t) cc_final: 0.8501 (m) REVERT: F 403 MET cc_start: 0.8388 (mmp) cc_final: 0.7743 (mtm) REVERT: F 455 TYR cc_start: 0.7657 (t80) cc_final: 0.7429 (t80) REVERT: F 725 ILE cc_start: 0.6727 (mt) cc_final: 0.6514 (mt) REVERT: F 766 LEU cc_start: 0.7065 (pt) cc_final: 0.6491 (mp) REVERT: F 817 LEU cc_start: 0.9106 (tp) cc_final: 0.8632 (tp) REVERT: F 821 ILE cc_start: 0.8371 (mt) cc_final: 0.8048 (mt) REVERT: F 850 GLU cc_start: 0.5534 (pm20) cc_final: 0.5083 (tt0) outliers start: 109 outliers final: 69 residues processed: 640 average time/residue: 0.1887 time to fit residues: 202.2936 Evaluate side-chains 561 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 488 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 70 optimal weight: 3.9990 chunk 353 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 0.0370 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 391 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 overall best weight: 2.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 747 HIS B 822 GLN B 849 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 822 GLN D 641 HIS ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 849 ASN F 195 GLN F 269 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103257 restraints weight = 68828.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105560 restraints weight = 41032.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107161 restraints weight = 28640.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108057 restraints weight = 22585.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108826 restraints weight = 19600.769| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33340 Z= 0.169 Angle : 0.682 10.716 44970 Z= 0.343 Chirality : 0.044 0.342 5093 Planarity : 0.005 0.072 5872 Dihedral : 8.130 146.036 4642 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.02 % Allowed : 14.70 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.79 (0.13), residues: 4053 helix: 0.57 (0.11), residues: 2355 sheet: -2.35 (0.25), residues: 398 loop : -1.85 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 556 TYR 0.021 0.002 TYR A 322 PHE 0.020 0.002 PHE A 749 TRP 0.024 0.002 TRP E 543 HIS 0.010 0.001 HIS B 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33321) covalent geometry : angle 0.68164 / 0.34 (44970) hydrogen bonds : bond 0.04524 / 3.06 ( 1827) hydrogen bonds : angle 4.99786 / 3.52 ( 5391) Misc. bond : bond 0.00415 / 0.21 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 526 time to evaluate : 1.328 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 481 GLN cc_start: 0.6459 (pt0) cc_final: 0.5733 (tt0) REVERT: A 528 ARG cc_start: 0.6814 (tpp-160) cc_final: 0.6126 (tpp-160) REVERT: A 562 MET cc_start: 0.8056 (mmm) cc_final: 0.7827 (mmm) REVERT: A 601 PHE cc_start: 0.8461 (m-80) cc_final: 0.8046 (m-80) REVERT: A 686 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8936 (m) REVERT: B 358 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7074 (pt0) REVERT: B 524 MET cc_start: 0.1594 (mmt) cc_final: -0.0612 (ptt) REVERT: B 685 ASP cc_start: 0.7335 (p0) cc_final: 0.7050 (p0) REVERT: B 700 THR cc_start: 0.8481 (m) cc_final: 0.7980 (p) REVERT: B 708 ASP cc_start: 0.7895 (t0) cc_final: 0.7320 (p0) REVERT: B 793 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 280 LEU cc_start: 0.9201 (tp) cc_final: 0.8852 (tp) REVERT: C 293 MET cc_start: 0.7974 (tpp) cc_final: 0.7292 (tmm) REVERT: C 405 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8497 (mt) REVERT: C 524 MET cc_start: 0.3985 (tpt) cc_final: 0.3656 (tpt) REVERT: C 558 LYS cc_start: 0.8745 (tttp) cc_final: 0.8534 (ttpt) REVERT: C 559 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 696 ASP cc_start: 0.8095 (m-30) cc_final: 0.7722 (m-30) REVERT: C 700 THR cc_start: 0.8333 (m) cc_final: 0.7869 (p) REVERT: C 705 ARG cc_start: 0.7515 (ptt90) cc_final: 0.7180 (ptt-90) REVERT: D 252 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6302 (ttt180) REVERT: D 533 ASP cc_start: 0.7584 (p0) cc_final: 0.6900 (m-30) REVERT: D 601 PHE cc_start: 0.8020 (m-80) cc_final: 0.7717 (m-80) REVERT: D 614 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9348 (tt) REVERT: D 636 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7098 (mt-10) REVERT: D 691 LEU cc_start: 0.8813 (mt) cc_final: 0.8572 (tp) REVERT: D 797 ASP cc_start: 0.7897 (p0) cc_final: 0.7591 (p0) REVERT: D 822 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: E 319 TYR cc_start: 0.8451 (t80) cc_final: 0.8044 (t80) REVERT: E 330 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7240 (tp30) REVERT: E 336 VAL cc_start: 0.9121 (t) cc_final: 0.8875 (t) REVERT: E 379 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7851 (ttt90) REVERT: E 396 GLU cc_start: 0.8444 (tt0) cc_final: 0.7863 (mt-10) REVERT: E 430 MET cc_start: 0.2189 (ppp) cc_final: 0.1670 (mmp) REVERT: E 543 TRP cc_start: 0.8560 (t-100) cc_final: 0.8209 (t-100) REVERT: E 621 PHE cc_start: 0.8667 (t80) cc_final: 0.8432 (t80) REVERT: E 633 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: E 677 ASP cc_start: 0.7631 (t0) cc_final: 0.7371 (t0) REVERT: E 681 LYS cc_start: 0.7665 (mptt) cc_final: 0.6986 (tptt) REVERT: E 683 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7202 (m170) REVERT: E 737 MET cc_start: 0.7363 (tpp) cc_final: 0.7116 (tpp) REVERT: E 783 TYR cc_start: 0.7588 (m-10) cc_final: 0.7369 (m-10) REVERT: F 403 MET cc_start: 0.8399 (mmp) cc_final: 0.7845 (mtm) REVERT: F 604 LEU cc_start: 0.7515 (mt) cc_final: 0.7193 (mt) REVERT: F 821 ILE cc_start: 0.8332 (mt) cc_final: 0.8050 (mt) outliers start: 138 outliers final: 74 residues processed: 613 average time/residue: 0.1991 time to fit residues: 205.4575 Evaluate side-chains 558 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 474 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 803 LEU Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 359 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 170 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 396 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 688 ASN B 192 GLN B 195 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 269 GLN D 502 GLN D 736 HIS D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 831 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102797 restraints weight = 69191.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105075 restraints weight = 41235.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106538 restraints weight = 28947.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107656 restraints weight = 23106.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108218 restraints weight = 19952.458| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33340 Z= 0.158 Angle : 0.673 18.766 44970 Z= 0.337 Chirality : 0.043 0.233 5093 Planarity : 0.004 0.056 5872 Dihedral : 8.027 166.532 4642 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.28 % Allowed : 15.54 % Favored : 80.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.52 (0.13), residues: 4053 helix: 0.80 (0.11), residues: 2364 sheet: -2.26 (0.25), residues: 408 loop : -1.76 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 819 TYR 0.031 0.002 TYR B 783 PHE 0.025 0.002 PHE C 729 TRP 0.021 0.002 TRP D 462 HIS 0.010 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (33321) covalent geometry : angle 0.67315 / 0.34 (44970) hydrogen bonds : bond 0.04391 / 2.96 ( 1827) hydrogen bonds : angle 4.88150 / 3.43 ( 5391) Misc. bond : bond 0.00352 / 0.18 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 501 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 481 GLN cc_start: 0.6521 (pt0) cc_final: 0.5903 (tt0) REVERT: A 528 ARG cc_start: 0.6884 (tpp-160) cc_final: 0.6115 (tpp-160) REVERT: A 562 MET cc_start: 0.8330 (mmm) cc_final: 0.7972 (mmm) REVERT: A 601 PHE cc_start: 0.8471 (m-80) cc_final: 0.8049 (m-80) REVERT: A 686 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (m) REVERT: B 358 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6908 (pt0) REVERT: B 524 MET cc_start: 0.1590 (mmt) cc_final: -0.0483 (ptt) REVERT: B 562 MET cc_start: 0.6294 (tmt) cc_final: 0.4785 (tmm) REVERT: B 668 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7737 (mmt180) REVERT: B 685 ASP cc_start: 0.7279 (p0) cc_final: 0.6961 (p0) REVERT: B 700 THR cc_start: 0.8489 (m) cc_final: 0.8057 (p) REVERT: B 708 ASP cc_start: 0.8000 (t0) cc_final: 0.7061 (p0) REVERT: B 758 ASP cc_start: 0.8397 (t0) cc_final: 0.8055 (t0) REVERT: B 843 VAL cc_start: 0.7454 (t) cc_final: 0.7124 (p) REVERT: C 280 LEU cc_start: 0.9258 (tp) cc_final: 0.8924 (tp) REVERT: C 293 MET cc_start: 0.7990 (tpp) cc_final: 0.7265 (tmm) REVERT: C 405 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 562 MET cc_start: 0.9022 (tpt) cc_final: 0.8739 (tpt) REVERT: C 696 ASP cc_start: 0.8074 (m-30) cc_final: 0.7735 (m-30) REVERT: C 700 THR cc_start: 0.8534 (m) cc_final: 0.8085 (p) REVERT: D 184 ASP cc_start: 0.7082 (p0) cc_final: 0.6811 (p0) REVERT: D 252 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6314 (ttt180) REVERT: D 601 PHE cc_start: 0.8027 (m-80) cc_final: 0.7734 (m-80) REVERT: D 627 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6655 (pp20) REVERT: D 632 ILE cc_start: 0.8915 (mm) cc_final: 0.8682 (mm) REVERT: D 634 MET cc_start: 0.8076 (mmt) cc_final: 0.7717 (mpp) REVERT: D 636 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6961 (mt-10) REVERT: D 797 ASP cc_start: 0.7877 (p0) cc_final: 0.7602 (p0) REVERT: E 233 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7417 (mmtt) REVERT: E 319 TYR cc_start: 0.8665 (t80) cc_final: 0.7666 (t80) REVERT: E 330 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7327 (tp30) REVERT: E 460 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7739 (tp30) REVERT: E 560 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8782 (mm) REVERT: E 633 ASP cc_start: 0.7255 (t0) cc_final: 0.6938 (m-30) REVERT: E 677 ASP cc_start: 0.7758 (t0) cc_final: 0.7509 (t0) REVERT: E 737 MET cc_start: 0.7397 (tpp) cc_final: 0.7088 (tpp) REVERT: F 329 LEU cc_start: 0.7841 (tt) cc_final: 0.7435 (mm) REVERT: F 403 MET cc_start: 0.8337 (mmp) cc_final: 0.7915 (mtm) REVERT: F 604 LEU cc_start: 0.7509 (mt) cc_final: 0.7164 (mt) REVERT: F 661 TYR cc_start: 0.6274 (m-80) cc_final: 0.6045 (m-80) REVERT: F 801 LYS cc_start: 0.8923 (pttp) cc_final: 0.8324 (mmtt) REVERT: F 821 ILE cc_start: 0.8420 (mt) cc_final: 0.8187 (mt) outliers start: 147 outliers final: 89 residues processed: 593 average time/residue: 0.1936 time to fit residues: 195.2717 Evaluate side-chains 546 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 452 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 723 ASP Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 285 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 703 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.134792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100840 restraints weight = 69452.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103137 restraints weight = 41811.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104694 restraints weight = 29408.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105602 restraints weight = 23369.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106294 restraints weight = 20347.755| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33340 Z= 0.196 Angle : 0.688 9.894 44970 Z= 0.348 Chirality : 0.045 0.221 5093 Planarity : 0.005 0.057 5872 Dihedral : 8.020 168.457 4642 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.22 % Allowed : 16.01 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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 (0.13), residues: 4053 helix: 0.79 (0.11), residues: 2379 sheet: -2.25 (0.26), residues: 388 loop : -1.74 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 789 TYR 0.022 0.002 TYR C 656 PHE 0.039 0.002 PHE C 729 TRP 0.021 0.002 TRP E 543 HIS 0.032 0.001 HIS D 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (33321) covalent geometry : angle 0.68800 / 0.35 (44970) hydrogen bonds : bond 0.04523 / 3.05 ( 1827) hydrogen bonds : angle 4.92078 / 3.46 ( 5391) Misc. bond : bond 0.00330 / 0.18 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 476 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7969 (t0) REVERT: A 399 SER cc_start: 0.9214 (m) cc_final: 0.9003 (p) REVERT: A 481 GLN cc_start: 0.6490 (pt0) cc_final: 0.5868 (tt0) REVERT: A 528 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6060 (tpp-160) REVERT: A 562 MET cc_start: 0.8352 (mmm) cc_final: 0.7975 (mmm) REVERT: A 601 PHE cc_start: 0.8638 (m-80) cc_final: 0.8231 (m-80) REVERT: B 358 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7050 (pt0) REVERT: B 524 MET cc_start: 0.1768 (mmt) cc_final: -0.0225 (ptt) REVERT: B 685 ASP cc_start: 0.7345 (p0) cc_final: 0.7058 (p0) REVERT: B 700 THR cc_start: 0.8562 (m) cc_final: 0.8173 (p) REVERT: B 708 ASP cc_start: 0.7790 (t0) cc_final: 0.7249 (p0) REVERT: B 843 VAL cc_start: 0.7455 (t) cc_final: 0.7116 (p) REVERT: C 181 ILE cc_start: 0.8967 (mp) cc_final: 0.8694 (mt) REVERT: C 280 LEU cc_start: 0.9228 (tp) cc_final: 0.9023 (tp) REVERT: C 293 MET cc_start: 0.7928 (tpp) cc_final: 0.7136 (tmm) REVERT: C 405 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 524 MET cc_start: 0.3943 (tpt) cc_final: 0.3523 (tpt) REVERT: C 559 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (tt) REVERT: C 696 ASP cc_start: 0.8110 (m-30) cc_final: 0.7870 (m-30) REVERT: C 700 THR cc_start: 0.8527 (m) cc_final: 0.8125 (p) REVERT: C 759 GLU cc_start: 0.8232 (pm20) cc_final: 0.7981 (pm20) REVERT: D 184 ASP cc_start: 0.7132 (p0) cc_final: 0.6868 (p0) REVERT: D 252 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6350 (ttp-170) REVERT: D 627 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6707 (pp20) REVERT: D 636 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 640 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8060 (ttpp) REVERT: D 797 ASP cc_start: 0.7971 (p0) cc_final: 0.7723 (p0) REVERT: E 184 ASP cc_start: 0.7815 (t0) cc_final: 0.7552 (t0) REVERT: E 233 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7444 (mmtt) REVERT: E 330 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7433 (tp30) REVERT: E 379 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7965 (ttt90) REVERT: E 396 GLU cc_start: 0.8406 (tt0) cc_final: 0.7466 (mt-10) REVERT: E 543 TRP cc_start: 0.8537 (t-100) cc_final: 0.7536 (m-90) REVERT: E 560 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8827 (mm) REVERT: E 633 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: E 677 ASP cc_start: 0.7885 (t0) cc_final: 0.7605 (t0) REVERT: E 681 LYS cc_start: 0.7560 (mptt) cc_final: 0.7040 (mptt) REVERT: E 695 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7094 (t0) REVERT: F 224 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7744 (tp) REVERT: F 329 LEU cc_start: 0.7847 (tt) cc_final: 0.7362 (mm) REVERT: F 403 MET cc_start: 0.8317 (mmp) cc_final: 0.7874 (mtm) REVERT: F 604 LEU cc_start: 0.7551 (mt) cc_final: 0.7267 (mt) REVERT: F 821 ILE cc_start: 0.8525 (mt) cc_final: 0.8273 (mt) outliers start: 145 outliers final: 99 residues processed: 566 average time/residue: 0.1902 time to fit residues: 182.2756 Evaluate side-chains 533 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 425 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 723 ASP Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 192 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 269 GLN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN D 748 ASN D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104466 restraints weight = 70264.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103888 restraints weight = 51987.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104422 restraints weight = 35457.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104791 restraints weight = 30809.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105019 restraints weight = 28037.933| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33340 Z= 0.163 Angle : 0.662 13.076 44970 Z= 0.333 Chirality : 0.044 0.289 5093 Planarity : 0.004 0.060 5872 Dihedral : 7.946 170.045 4642 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.73 % Allowed : 17.32 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.33 (0.13), residues: 4053 helix: 0.89 (0.11), residues: 2387 sheet: -2.17 (0.26), residues: 386 loop : -1.63 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 789 TYR 0.020 0.002 TYR C 656 PHE 0.031 0.002 PHE C 729 TRP 0.016 0.002 TRP E 543 HIS 0.015 0.001 HIS F 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (33321) covalent geometry : angle 0.66200 / 0.33 (44970) hydrogen bonds : bond 0.04331 / 2.92 ( 1827) hydrogen bonds : angle 4.83106 / 3.40 ( 5391) Misc. bond : bond 0.00264 / 0.15 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 458 time to evaluate : 1.187 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 392 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7999 (t0) REVERT: A 399 SER cc_start: 0.9184 (m) cc_final: 0.8954 (p) REVERT: A 481 GLN cc_start: 0.6749 (pt0) cc_final: 0.6156 (tt0) REVERT: A 519 LEU cc_start: 0.8205 (mt) cc_final: 0.7838 (tp) REVERT: A 562 MET cc_start: 0.8464 (mmm) cc_final: 0.8061 (mmm) REVERT: A 601 PHE cc_start: 0.8656 (m-80) cc_final: 0.8267 (m-80) REVERT: B 358 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6997 (pt0) REVERT: B 524 MET cc_start: 0.1810 (mmt) cc_final: 0.0041 (ptt) REVERT: B 685 ASP cc_start: 0.7421 (p0) cc_final: 0.7072 (p0) REVERT: B 700 THR cc_start: 0.8559 (m) cc_final: 0.8152 (p) REVERT: B 708 ASP cc_start: 0.7851 (t0) cc_final: 0.7345 (p0) REVERT: B 843 VAL cc_start: 0.7768 (t) cc_final: 0.7451 (p) REVERT: C 181 ILE cc_start: 0.9020 (mp) cc_final: 0.8764 (mt) REVERT: C 254 GLU cc_start: 0.8522 (tp30) cc_final: 0.8280 (tp30) REVERT: C 405 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8348 (mt) REVERT: C 524 MET cc_start: 0.3981 (tpt) cc_final: 0.3576 (tpt) REVERT: C 562 MET cc_start: 0.9059 (tpt) cc_final: 0.8683 (tpt) REVERT: C 696 ASP cc_start: 0.8160 (m-30) cc_final: 0.7950 (m-30) REVERT: C 700 THR cc_start: 0.8551 (m) cc_final: 0.8228 (p) REVERT: D 184 ASP cc_start: 0.7137 (p0) cc_final: 0.6875 (p0) REVERT: D 252 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6214 (ttt180) REVERT: D 627 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6725 (pp20) REVERT: D 634 MET cc_start: 0.8255 (mmt) cc_final: 0.7861 (mpp) REVERT: D 636 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6897 (mt-10) REVERT: D 640 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7919 (ttpp) REVERT: D 692 GLN cc_start: 0.7975 (tt0) cc_final: 0.7340 (tt0) REVERT: D 797 ASP cc_start: 0.8100 (p0) cc_final: 0.7842 (p0) REVERT: E 184 ASP cc_start: 0.7941 (t0) cc_final: 0.7676 (t0) REVERT: E 233 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7549 (mmtt) REVERT: E 319 TYR cc_start: 0.8509 (t80) cc_final: 0.8124 (t80) REVERT: E 330 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7309 (tp30) REVERT: E 560 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8784 (mm) REVERT: E 633 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: E 677 ASP cc_start: 0.7906 (t0) cc_final: 0.7699 (t0) REVERT: E 752 GLU cc_start: 0.6600 (pm20) cc_final: 0.6320 (pm20) REVERT: E 821 ILE cc_start: 0.8712 (mp) cc_final: 0.8448 (mp) REVERT: F 283 MET cc_start: 0.8311 (tpp) cc_final: 0.7755 (tpp) REVERT: F 329 LEU cc_start: 0.8107 (tt) cc_final: 0.7481 (mm) REVERT: F 359 LEU cc_start: 0.8462 (pp) cc_final: 0.7791 (mm) REVERT: F 403 MET cc_start: 0.8282 (mmp) cc_final: 0.7994 (mtm) REVERT: F 524 MET cc_start: 0.5701 (mmm) cc_final: 0.5336 (mmm) REVERT: F 604 LEU cc_start: 0.7631 (mt) cc_final: 0.7416 (mt) REVERT: F 801 LYS cc_start: 0.8919 (pttp) cc_final: 0.8379 (mmtt) REVERT: F 821 ILE cc_start: 0.8534 (mt) cc_final: 0.8250 (mt) outliers start: 128 outliers final: 93 residues processed: 536 average time/residue: 0.1873 time to fit residues: 170.5625 Evaluate side-chains 524 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 426 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 PHE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 23 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 747 HIS B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 692 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN F 192 GLN F 195 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106450 restraints weight = 69261.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105947 restraints weight = 51577.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106270 restraints weight = 36071.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106828 restraints weight = 33995.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107500 restraints weight = 27718.329| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33340 Z= 0.136 Angle : 0.648 11.254 44970 Z= 0.324 Chirality : 0.043 0.318 5093 Planarity : 0.004 0.060 5872 Dihedral : 7.836 170.472 4642 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.08 % Allowed : 18.31 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.15 (0.14), residues: 4053 helix: 1.02 (0.11), residues: 2388 sheet: -2.09 (0.26), residues: 386 loop : -1.54 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 789 TYR 0.021 0.001 TYR C 656 PHE 0.017 0.001 PHE D 623 TRP 0.024 0.002 TRP E 543 HIS 0.014 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (33321) covalent geometry : angle 0.64827 / 0.32 (44970) hydrogen bonds : bond 0.04146 / 2.79 ( 1827) hydrogen bonds : angle 4.74496 / 3.33 ( 5391) Misc. bond : bond 0.00245 / 0.14 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 476 time to evaluate : 1.369 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 265 ASP cc_start: 0.7027 (m-30) cc_final: 0.6656 (t70) REVERT: A 392 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7956 (t0) REVERT: A 481 GLN cc_start: 0.6649 (pt0) cc_final: 0.6100 (tt0) REVERT: A 519 LEU cc_start: 0.8180 (mt) cc_final: 0.7817 (tp) REVERT: A 551 MET cc_start: 0.5661 (ttp) cc_final: 0.3091 (tmm) REVERT: A 601 PHE cc_start: 0.8624 (m-80) cc_final: 0.8275 (m-80) REVERT: A 602 LEU cc_start: 0.8850 (tp) cc_final: 0.8608 (tt) REVERT: A 658 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5885 (mm-30) REVERT: B 192 GLN cc_start: 0.8419 (mt0) cc_final: 0.8202 (tt0) REVERT: B 358 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6991 (pt0) REVERT: B 524 MET cc_start: 0.1893 (mmt) cc_final: 0.0142 (ptt) REVERT: B 562 MET cc_start: 0.6075 (tmt) cc_final: 0.4715 (tmm) REVERT: B 685 ASP cc_start: 0.7426 (p0) cc_final: 0.7122 (p0) REVERT: B 700 THR cc_start: 0.8430 (m) cc_final: 0.7981 (p) REVERT: B 708 ASP cc_start: 0.7803 (t0) cc_final: 0.7296 (p0) REVERT: B 843 VAL cc_start: 0.7810 (t) cc_final: 0.7482 (p) REVERT: C 254 GLU cc_start: 0.8503 (tp30) cc_final: 0.8267 (tp30) REVERT: C 293 MET cc_start: 0.8191 (mmm) cc_final: 0.7361 (tmm) REVERT: C 396 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 405 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8364 (mt) REVERT: C 524 MET cc_start: 0.4248 (tpt) cc_final: 0.3874 (tpt) REVERT: C 562 MET cc_start: 0.8955 (tpt) cc_final: 0.8740 (tpt) REVERT: C 700 THR cc_start: 0.8545 (m) cc_final: 0.8315 (p) REVERT: C 722 SER cc_start: 0.7962 (m) cc_final: 0.7750 (t) REVERT: C 817 LEU cc_start: 0.9229 (tp) cc_final: 0.9011 (tp) REVERT: D 184 ASP cc_start: 0.7081 (p0) cc_final: 0.6785 (p0) REVERT: D 252 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6174 (ttp-170) REVERT: D 627 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6694 (pp20) REVERT: D 640 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7914 (ttpp) REVERT: D 657 GLU cc_start: 0.7796 (pm20) cc_final: 0.7325 (pm20) REVERT: D 691 LEU cc_start: 0.8604 (tp) cc_final: 0.7935 (tt) REVERT: E 184 ASP cc_start: 0.8018 (t0) cc_final: 0.7734 (t0) REVERT: E 233 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7562 (mmtt) REVERT: E 330 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7286 (tp30) REVERT: E 560 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8793 (mm) REVERT: E 633 ASP cc_start: 0.7640 (t0) cc_final: 0.7159 (m-30) REVERT: E 677 ASP cc_start: 0.7936 (t0) cc_final: 0.7604 (t0) REVERT: E 821 ILE cc_start: 0.8734 (mp) cc_final: 0.8520 (mp) REVERT: F 329 LEU cc_start: 0.7966 (tt) cc_final: 0.7485 (mm) REVERT: F 359 LEU cc_start: 0.8426 (pp) cc_final: 0.7796 (mm) REVERT: F 392 ASP cc_start: 0.7388 (t0) cc_final: 0.7073 (t0) REVERT: F 403 MET cc_start: 0.8206 (mmp) cc_final: 0.7967 (mtm) REVERT: F 661 TYR cc_start: 0.6389 (m-80) cc_final: 0.5833 (m-80) REVERT: F 801 LYS cc_start: 0.8866 (pttp) cc_final: 0.8313 (mmtt) REVERT: F 821 ILE cc_start: 0.8489 (mt) cc_final: 0.8148 (mt) outliers start: 106 outliers final: 81 residues processed: 543 average time/residue: 0.1897 time to fit residues: 174.8724 Evaluate side-chains 512 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 426 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 116 optimal weight: 0.0170 chunk 208 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106472 restraints weight = 69483.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107531 restraints weight = 45409.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108403 restraints weight = 28755.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108833 restraints weight = 26863.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108821 restraints weight = 23422.544| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33340 Z= 0.127 Angle : 0.656 11.843 44970 Z= 0.327 Chirality : 0.043 0.274 5093 Planarity : 0.004 0.099 5872 Dihedral : 7.751 171.719 4642 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.74 % Allowed : 18.95 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 4053 helix: 1.11 (0.11), residues: 2394 sheet: -2.03 (0.26), residues: 393 loop : -1.45 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 556 TYR 0.021 0.001 TYR C 656 PHE 0.018 0.001 PHE F 621 TRP 0.019 0.001 TRP E 543 HIS 0.010 0.001 HIS C 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (33321) covalent geometry : angle 0.65572 / 0.33 (44970) hydrogen bonds : bond 0.03980 / 2.68 ( 1827) hydrogen bonds : angle 4.66187 / 3.27 ( 5391) Misc. bond : bond 0.00233 / 0.13 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 479 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ASP cc_start: 0.7064 (m-30) cc_final: 0.6664 (t70) REVERT: A 392 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 481 GLN cc_start: 0.6617 (pt0) cc_final: 0.6069 (tt0) REVERT: A 519 LEU cc_start: 0.8225 (mt) cc_final: 0.7900 (tp) REVERT: A 528 ARG cc_start: 0.6649 (tpp-160) cc_final: 0.4689 (mmm-85) REVERT: A 601 PHE cc_start: 0.8593 (m-80) cc_final: 0.8228 (m-80) REVERT: A 602 LEU cc_start: 0.8792 (tp) cc_final: 0.8569 (tt) REVERT: B 241 ASP cc_start: 0.7949 (t70) cc_final: 0.7166 (t0) REVERT: B 358 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7147 (pt0) REVERT: B 524 MET cc_start: 0.1935 (mmt) cc_final: 0.0362 (ptt) REVERT: B 562 MET cc_start: 0.5945 (tmt) cc_final: 0.4653 (tmm) REVERT: B 700 THR cc_start: 0.8321 (m) cc_final: 0.7984 (p) REVERT: B 708 ASP cc_start: 0.7700 (t0) cc_final: 0.7146 (p0) REVERT: B 843 VAL cc_start: 0.7823 (t) cc_final: 0.7487 (p) REVERT: C 254 GLU cc_start: 0.8543 (tp30) cc_final: 0.8302 (tp30) REVERT: C 350 LEU cc_start: 0.9287 (mt) cc_final: 0.8931 (mt) REVERT: C 405 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 700 THR cc_start: 0.8611 (m) cc_final: 0.8269 (p) REVERT: D 184 ASP cc_start: 0.6975 (p0) cc_final: 0.6710 (p0) REVERT: D 252 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.5967 (ttp-170) REVERT: D 627 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6685 (pp20) REVERT: D 640 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7929 (ttpp) REVERT: D 647 VAL cc_start: 0.9282 (p) cc_final: 0.9024 (t) REVERT: D 691 LEU cc_start: 0.8558 (tp) cc_final: 0.8134 (tp) REVERT: E 184 ASP cc_start: 0.7995 (t0) cc_final: 0.7662 (t0) REVERT: E 186 GLU cc_start: 0.7989 (mp0) cc_final: 0.7712 (mp0) REVERT: E 233 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7622 (mmtt) REVERT: E 330 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7305 (tp30) REVERT: E 379 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8005 (ttt90) REVERT: E 570 VAL cc_start: 0.9085 (t) cc_final: 0.8868 (p) REVERT: E 633 ASP cc_start: 0.7564 (t0) cc_final: 0.6955 (m-30) REVERT: E 677 ASP cc_start: 0.7924 (t0) cc_final: 0.7589 (t0) REVERT: E 821 ILE cc_start: 0.8808 (mp) cc_final: 0.8488 (mp) REVERT: F 299 LEU cc_start: 0.8420 (mp) cc_final: 0.7833 (pp) REVERT: F 329 LEU cc_start: 0.7994 (tt) cc_final: 0.7489 (mm) REVERT: F 359 LEU cc_start: 0.8442 (pp) cc_final: 0.7804 (mm) REVERT: F 392 ASP cc_start: 0.7432 (t0) cc_final: 0.7116 (t0) REVERT: F 403 MET cc_start: 0.8282 (mmp) cc_final: 0.8013 (mtm) REVERT: F 443 MET cc_start: 0.6213 (ppp) cc_final: 0.5895 (ppp) REVERT: F 453 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7954 (ptt90) REVERT: F 661 TYR cc_start: 0.6369 (m-80) cc_final: 0.5776 (m-80) REVERT: F 696 ASP cc_start: 0.7552 (t0) cc_final: 0.7323 (t70) REVERT: F 801 LYS cc_start: 0.8899 (pttp) cc_final: 0.8295 (mmtm) REVERT: F 817 LEU cc_start: 0.8764 (tp) cc_final: 0.8557 (tt) REVERT: F 821 ILE cc_start: 0.8374 (mt) cc_final: 0.8132 (mt) outliers start: 94 outliers final: 64 residues processed: 541 average time/residue: 0.1982 time to fit residues: 181.6321 Evaluate side-chains 503 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 435 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 403 optimal weight: 8.9990 chunk 343 optimal weight: 0.6980 chunk 303 optimal weight: 7.9990 chunk 314 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 79 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 395 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107659 restraints weight = 69135.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108473 restraints weight = 48458.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108658 restraints weight = 33191.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109352 restraints weight = 30864.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109599 restraints weight = 27114.695| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33340 Z= 0.128 Angle : 0.668 10.445 44970 Z= 0.332 Chirality : 0.043 0.261 5093 Planarity : 0.004 0.060 5872 Dihedral : 7.704 171.440 4642 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.30 % Allowed : 19.67 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 4053 helix: 1.19 (0.11), residues: 2382 sheet: -1.99 (0.26), residues: 393 loop : -1.39 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 845 TYR 0.022 0.001 TYR D 656 PHE 0.034 0.002 PHE A 753 TRP 0.016 0.001 TRP E 543 HIS 0.021 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (33321) covalent geometry : angle 0.66818 / 0.33 (44970) hydrogen bonds : bond 0.03909 / 2.62 ( 1827) hydrogen bonds : angle 4.62492 / 3.24 ( 5391) Misc. bond : bond 0.00226 / 0.13 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 473 time to evaluate : 1.029 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 186 GLU cc_start: 0.8330 (mp0) cc_final: 0.7536 (mp0) REVERT: A 265 ASP cc_start: 0.7110 (m-30) cc_final: 0.6808 (t70) REVERT: A 392 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (t0) REVERT: A 481 GLN cc_start: 0.6615 (pt0) cc_final: 0.6086 (tt0) REVERT: A 519 LEU cc_start: 0.8218 (mt) cc_final: 0.7873 (tp) REVERT: A 524 MET cc_start: 0.1393 (tpp) cc_final: 0.1172 (ttm) REVERT: A 528 ARG cc_start: 0.6871 (tpp-160) cc_final: 0.4777 (mmm-85) REVERT: A 601 PHE cc_start: 0.8587 (m-80) cc_final: 0.8224 (m-80) REVERT: B 241 ASP cc_start: 0.7963 (t70) cc_final: 0.7297 (t0) REVERT: B 358 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7172 (pt0) REVERT: B 395 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7683 (t70) REVERT: B 524 MET cc_start: 0.1768 (mmt) cc_final: 0.0282 (ptt) REVERT: B 700 THR cc_start: 0.8452 (m) cc_final: 0.8117 (p) REVERT: B 708 ASP cc_start: 0.7699 (t0) cc_final: 0.7178 (p0) REVERT: B 759 GLU cc_start: 0.5862 (mp0) cc_final: 0.5547 (mp0) REVERT: B 843 VAL cc_start: 0.7745 (t) cc_final: 0.7417 (p) REVERT: C 254 GLU cc_start: 0.8582 (tp30) cc_final: 0.8361 (tp30) REVERT: C 293 MET cc_start: 0.7744 (mmm) cc_final: 0.7325 (tmm) REVERT: C 350 LEU cc_start: 0.9259 (mt) cc_final: 0.8818 (mt) REVERT: C 396 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 405 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 524 MET cc_start: 0.3696 (tpt) cc_final: 0.3008 (tpt) REVERT: C 692 GLN cc_start: 0.7150 (mt0) cc_final: 0.6852 (mt0) REVERT: C 700 THR cc_start: 0.8638 (m) cc_final: 0.8284 (p) REVERT: D 184 ASP cc_start: 0.7020 (p0) cc_final: 0.6750 (p0) REVERT: D 252 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.5993 (ttp-170) REVERT: D 552 MET cc_start: 0.7113 (ppp) cc_final: 0.6435 (ppp) REVERT: D 627 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6735 (pp20) REVERT: D 647 VAL cc_start: 0.9272 (p) cc_final: 0.8964 (t) REVERT: D 657 GLU cc_start: 0.7636 (pm20) cc_final: 0.7192 (pm20) REVERT: D 691 LEU cc_start: 0.8541 (tp) cc_final: 0.8186 (tp) REVERT: E 184 ASP cc_start: 0.8010 (t0) cc_final: 0.7652 (t0) REVERT: E 233 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7666 (mmtt) REVERT: E 330 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7357 (tp30) REVERT: E 621 PHE cc_start: 0.8385 (t80) cc_final: 0.8094 (t80) REVERT: E 677 ASP cc_start: 0.7916 (t0) cc_final: 0.7631 (t0) REVERT: E 681 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7254 (mptt) REVERT: E 821 ILE cc_start: 0.8742 (mp) cc_final: 0.8441 (mp) REVERT: F 329 LEU cc_start: 0.7906 (tt) cc_final: 0.7392 (mm) REVERT: F 359 LEU cc_start: 0.8423 (pp) cc_final: 0.7776 (mm) REVERT: F 392 ASP cc_start: 0.7336 (t0) cc_final: 0.7086 (t0) REVERT: F 403 MET cc_start: 0.8227 (mmp) cc_final: 0.8026 (mtm) REVERT: F 443 MET cc_start: 0.6126 (ppp) cc_final: 0.5854 (ppp) REVERT: F 453 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.7933 (ptt90) REVERT: F 661 TYR cc_start: 0.6352 (m-80) cc_final: 0.5819 (m-80) REVERT: F 696 ASP cc_start: 0.7532 (t0) cc_final: 0.7306 (t0) REVERT: F 756 ARG cc_start: 0.6033 (ttp-170) cc_final: 0.5147 (ptp-170) REVERT: F 801 LYS cc_start: 0.8909 (pttp) cc_final: 0.8320 (mmtm) REVERT: F 821 ILE cc_start: 0.8396 (mt) cc_final: 0.8178 (mt) outliers start: 79 outliers final: 66 residues processed: 528 average time/residue: 0.1912 time to fit residues: 173.2728 Evaluate side-chains 508 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 438 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 303 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 192 optimal weight: 0.0870 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 347 optimal weight: 10.0000 chunk 341 optimal weight: 2.9990 overall best weight: 2.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 321 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 831 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104227 restraints weight = 69773.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104875 restraints weight = 45251.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105246 restraints weight = 33048.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105663 restraints weight = 29635.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105807 restraints weight = 27482.077| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33340 Z= 0.183 Angle : 0.703 10.159 44970 Z= 0.352 Chirality : 0.045 0.250 5093 Planarity : 0.004 0.059 5872 Dihedral : 7.796 169.265 4642 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.42 % Allowed : 19.73 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 4053 helix: 1.15 (0.11), residues: 2394 sheet: -2.03 (0.26), residues: 395 loop : -1.37 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 756 TYR 0.025 0.002 TYR D 656 PHE 0.028 0.002 PHE A 753 TRP 0.018 0.002 TRP E 543 HIS 0.024 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (33321) covalent geometry : angle 0.70346 / 0.35 (44970) hydrogen bonds : bond 0.04222 / 2.85 ( 1827) hydrogen bonds : angle 4.67940 / 3.28 ( 5391) Misc. bond : bond 0.00267 / 0.16 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5828.60 seconds wall clock time: 101 minutes 16.71 seconds (6076.71 seconds total)