Starting phenix.real_space_refine on Mon Sep 14 07:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs4_4621/09_2026/6qs4_4621.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 107 5.16 5 C 17996 2.51 5 N 5225 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 28839 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 6.70, per 1000 atoms: 0.23 Number of scatterers: 28839 At special positions: 0 Unit cell: (117.6, 142.8, 156.45, 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 107 16.00 P 31 15.00 O 5480 8.00 N 5225 7.00 C 17996 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 27 sheets defined 59.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.597A pdb=" N TYR A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.356A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.762A pdb=" N MET A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 285' Processing helix chain 'A' and resid 295 through 306 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 342 through 362 removed outlier: 4.733A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.782A pdb=" N ILE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.840A pdb=" N GLY A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.888A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 679 through 682 Processing helix chain 'A' and resid 683 through 684 No H-bonds generated for 'chain 'A' and resid 683 through 684' Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.615A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 727 removed outlier: 3.656A pdb=" N ILE A 725 " --> pdb=" O GLY A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.653A pdb=" N MET A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.696A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 814 through 835 removed outlier: 4.194A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Proline residue: A 828 - end of helix removed outlier: 3.620A pdb=" N GLN A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) 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 225 removed outlier: 3.703A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.949A pdb=" N GLY B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 Proline residue: B 301 - end of helix removed outlier: 4.081A 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 331 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 387 through 408 removed outlier: 4.094A pdb=" N LYS B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.803A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 624 Processing helix chain 'B' and resid 635 through 638 removed outlier: 4.024A pdb=" N MET B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 635 through 638' Processing helix chain 'B' and resid 642 through 648 Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.817A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 659 " --> pdb=" O TYR B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.976A pdb=" N ARG B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.515A pdb=" N PHE B 687 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.560A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.639A pdb=" N ARG B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 Processing helix chain 'B' and resid 814 through 827 Processing helix chain 'B' and resid 827 through 835 Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 253 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.653A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.677A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.561A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.618A pdb=" N ARG C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.658A pdb=" N THR C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.704A pdb=" N ILE C 391 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 428 Processing helix chain 'C' and resid 444 through 465 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 552 through 561 removed outlier: 3.800A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 removed outlier: 3.720A pdb=" N HIS C 567 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.587A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 642 through 648 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.736A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 668 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 Processing helix chain 'C' and resid 750 through 755 removed outlier: 3.504A pdb=" N ASN C 755 " --> pdb=" O PRO C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 790 removed outlier: 4.117A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 removed outlier: 3.658A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.612A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.793A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.684A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.508A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.821A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 342 through 362 Processing helix chain 'D' and resid 366 through 380 removed outlier: 3.830A pdb=" N ILE D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 429 Processing helix chain 'D' and resid 444 through 465 Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.712A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.618A 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 589 Processing helix chain 'D' and resid 610 through 623 Processing helix chain 'D' and resid 633 through 637 Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.502A pdb=" N GLU D 658 " --> pdb=" O GLY D 655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 661 through 669 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.650A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 806 removed outlier: 3.648A pdb=" N LEU D 800 " --> pdb=" O SER D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 835 removed outlier: 3.624A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 164 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 removed outlier: 3.582A pdb=" N LYS E 233 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 247 removed outlier: 3.867A 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 295 through 304 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.694A pdb=" N GLU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 331' Processing helix chain 'E' and resid 342 through 362 Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'E' and resid 444 through 466 Processing helix chain 'E' and resid 532 through 544 removed outlier: 3.608A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.822A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 623 removed outlier: 3.573A pdb=" N LEU E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 641 No H-bonds generated for 'chain 'E' and resid 639 through 641' Processing helix chain 'E' and resid 642 through 647 Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.714A pdb=" N GLY E 659 " --> pdb=" O TYR E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 669 removed outlier: 3.815A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.529A pdb=" N LYS E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 685 No H-bonds generated for 'chain 'E' and resid 683 through 685' Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 733 through 749 Processing helix chain 'E' and resid 750 through 757 removed outlier: 4.147A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 790 removed outlier: 3.564A pdb=" N ARG E 789 " --> pdb=" O ARG E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 807 Processing helix chain 'E' and resid 814 through 825 removed outlier: 3.558A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 835 Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.512A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.785A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 294 through 304 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.971A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 406 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 558 through 560 No H-bonds generated for 'chain 'F' and resid 558 through 560' Processing helix chain 'F' and resid 561 through 570 removed outlier: 3.668A pdb=" N GLU F 565 " --> pdb=" O ARG F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 589 Processing helix chain 'F' and resid 610 through 622 Processing helix chain 'F' and resid 639 through 641 No H-bonds generated for 'chain 'F' and resid 639 through 641' Processing helix chain 'F' and resid 642 through 647 Processing helix chain 'F' and resid 660 through 669 removed outlier: 3.532A pdb=" N ALA F 665 " --> pdb=" O TYR F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 697 Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.664A pdb=" N ILE F 771 " --> pdb=" O GLY F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 807 Processing helix chain 'F' and resid 814 through 834 removed outlier: 3.507A pdb=" N LYS F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 239 removed outlier: 8.292A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 629 through 633 removed outlier: 5.907A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 714 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 716 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 761 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 698 through 700 Processing sheet with id=AA4, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.899A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 633 removed outlier: 3.764A pdb=" N ASP B 677 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 713 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 599 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET B 716 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AA8, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.445A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 278 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C 311 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 275 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 205 Processing sheet with id=AB1, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.726A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 630 through 631 removed outlier: 6.636A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 674 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR C 717 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 676 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB4, first strand: chain 'C' and resid 843 through 848 removed outlier: 3.512A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.400A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 313 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 630 through 631 removed outlier: 6.350A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR D 717 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE D 601 " --> pdb=" O MET D 716 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 602 " --> pdb=" O GLU D 759 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 698 through 700 removed outlier: 3.869A pdb=" N LEU D 699 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.801A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.223A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.046A pdb=" N PHE E 601 " --> pdb=" O MET E 716 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.816A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 792 through 795 removed outlier: 6.797A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 165 through 167 Processing sheet with id=AC5, first strand: chain 'F' and resid 203 through 206 Processing sheet with id=AC6, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.270A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 629 through 631 removed outlier: 6.046A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 698 through 700 Processing sheet with id=AC9, first strand: chain 'F' and resid 793 through 795 removed outlier: 7.670A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1438 hydrogen bonds defined for protein. 4245 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: 6.52 Time building geometry restraints manager: 3.39 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: 10204 1.36 - 1.51: 8221 1.51 - 1.65: 10651 1.65 - 1.80: 156 1.80 - 1.95: 37 Bond restraints: 29269 Sorted by residual: bond pdb=" O1B AGS D1003 " pdb=" PB AGS D1003 " ideal model delta sigma weight residual 1.481 1.556 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB PHE C 687 " pdb=" CG PHE C 687 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.65e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CG GLN C 385 " pdb=" CD GLN C 385 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.35e+00 bond pdb=" CB GLU D 613 " pdb=" CG GLU D 613 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.11e+00 ... (remaining 29264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 38814 3.18 - 6.35: 645 6.35 - 9.53: 73 9.53 - 12.70: 19 12.70 - 15.88: 4 Bond angle restraints: 39555 Sorted by residual: angle pdb=" C HIS C 641 " pdb=" N SER C 642 " pdb=" CA SER C 642 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLY E 610 " pdb=" N LYS E 611 " pdb=" CA LYS E 611 " ideal model delta sigma weight residual 120.88 112.88 8.00 1.62e+00 3.81e-01 2.44e+01 angle pdb=" C ARG B 645 " pdb=" N LEU B 646 " pdb=" CA LEU B 646 " ideal model delta sigma weight residual 121.66 113.49 8.17 1.76e+00 3.23e-01 2.15e+01 angle pdb=" C PHE B 749 " pdb=" N ARG B 750 " pdb=" CA ARG B 750 " ideal model delta sigma weight residual 120.97 134.06 -13.09 2.84e+00 1.24e-01 2.13e+01 angle pdb=" C MET D 293 " pdb=" N ASP D 294 " pdb=" CA ASP D 294 " ideal model delta sigma weight residual 122.44 116.97 5.47 1.19e+00 7.06e-01 2.11e+01 ... (remaining 39550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 17548 24.80 - 49.61: 361 49.61 - 74.41: 22 74.41 - 99.21: 11 99.21 - 124.02: 2 Dihedral angle restraints: 17944 sinusoidal: 7535 harmonic: 10409 Sorted by residual: dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual 300.00 175.98 124.02 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N VAL C 654 " pdb=" CA VAL C 654 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 17941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3210 0.060 - 0.120: 1048 0.120 - 0.179: 189 0.179 - 0.239: 22 0.239 - 0.299: 4 Chirality restraints: 4473 Sorted by residual: chirality pdb=" PB AGS D1003 " pdb=" O2B AGS D1003 " pdb=" O3A AGS D1003 " pdb=" O3B AGS D1003 " both_signs ideal model delta sigma weight residual True 3.18 3.48 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" PB AGS D1001 " pdb=" O2B AGS D1001 " pdb=" O3A AGS D1001 " pdb=" O3B AGS D1001 " both_signs ideal model delta sigma weight residual True 3.18 2.91 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE E 571 " pdb=" CA ILE E 571 " pdb=" CG1 ILE E 571 " pdb=" CG2 ILE E 571 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4470 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 543 " -0.037 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP E 543 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 543 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 543 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 543 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 543 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 543 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 543 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 543 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 543 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 367 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO C 368 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 368 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 368 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 684 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.037 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5675 2.77 - 3.30: 27398 3.30 - 3.83: 48520 3.83 - 4.37: 56355 4.37 - 4.90: 94771 Nonbonded interactions: 232719 Sorted by model distance: nonbonded pdb=" O GLN D 195 " pdb=" OG SER E 399 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR B 656 " pdb=" OE1 GLU C 658 " model vdw 2.239 3.040 nonbonded pdb=" O1B AGS D1003 " pdb=" O2A AGS D1003 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 656 " pdb=" OE1 GLU B 658 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP B 677 " pdb=" OG1 THR B 717 " model vdw 2.252 3.040 ... (remaining 232714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and resid 159 through 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: 1.810 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: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.010 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 : 0.009 0.100 29279 Z= 0.395 Angle : 1.074 15.878 39555 Z= 0.572 Chirality : 0.058 0.299 4473 Planarity : 0.008 0.072 5164 Dihedral : 10.544 124.017 11228 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.10 % Allowed : 1.06 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.77 (0.11), residues: 3578 helix: -2.25 (0.09), residues: 1888 sheet: -2.85 (0.25), residues: 356 loop : -2.50 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 332 TYR 0.030 0.003 TYR B 322 PHE 0.037 0.004 PHE D 763 TRP 0.080 0.006 TRP E 543 HIS 0.014 0.002 HIS F 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.39 (29269) covalent geometry : angle 1.07394 / 0.57 (39555) hydrogen bonds : bond 0.16470 / 11.03 ( 1438) hydrogen bonds : angle 7.77426 / 5.53 ( 4245) Misc. bond : bond 0.00815 / 0.38 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 612 time to evaluate : 1.248 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: 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: 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 194 LEU cc_start: 0.8506 (mt) cc_final: 0.8232 (tp) REVERT: A 293 MET cc_start: 0.0194 (tpt) cc_final: -0.0891 (mmt) REVERT: A 723 ASP cc_start: 0.9453 (m-30) cc_final: 0.9215 (p0) REVERT: B 293 MET cc_start: 0.4802 (mmt) cc_final: 0.4521 (mmt) REVERT: B 602 LEU cc_start: 0.7729 (tp) cc_final: 0.6920 (tp) REVERT: E 350 LEU cc_start: 0.8124 (mt) cc_final: 0.7910 (tp) REVERT: F 403 MET cc_start: 0.9102 (mtp) cc_final: 0.8203 (tpt) REVERT: F 661 TYR cc_start: 0.7678 (t80) cc_final: 0.7448 (t80) outliers start: 3 outliers final: 0 residues processed: 615 average time/residue: 0.2338 time to fit residues: 216.9997 Evaluate side-chains 335 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 281 HIS ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS A 641 HIS A 726 GLN A 770 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN A 849 ASN A 858 HIS B 192 GLN B 195 GLN B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 824 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 HIS C 221 GLN C 297 ASN C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN D 192 GLN D 195 GLN D 421 GLN D 567 HIS D 641 HIS D 711 ASN D 794 HIS D 822 GLN D 858 HIS E 297 ASN E 321 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 567 HIS E 641 HIS E 692 GLN E 822 GLN E 858 HIS F 281 HIS F 297 ASN F 309 HIS F 321 GLN F 620 ASN F 688 ASN F 726 GLN F 857 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.048133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034883 restraints weight = 186059.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035240 restraints weight = 164841.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035486 restraints weight = 150637.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035701 restraints weight = 141110.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035879 restraints weight = 134512.079| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29279 Z= 0.185 Angle : 0.747 12.019 39555 Z= 0.380 Chirality : 0.046 0.230 4473 Planarity : 0.006 0.066 5164 Dihedral : 8.601 117.133 4094 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3578 helix: -0.66 (0.11), residues: 1968 sheet: -2.52 (0.24), residues: 378 loop : -1.87 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 379 TYR 0.024 0.002 TYR A 812 PHE 0.032 0.003 PHE C 333 TRP 0.022 0.002 TRP E 543 HIS 0.007 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (29269) covalent geometry : angle 0.74688 / 0.38 (39555) hydrogen bonds : bond 0.05196 / 3.49 ( 1438) hydrogen bonds : angle 5.92280 / 4.23 ( 4245) Misc. bond : bond 0.00299 / 0.14 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 392 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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 293 MET cc_start: -0.0570 (tpt) cc_final: -0.1311 (mmt) REVERT: A 330 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8255 (mm-30) REVERT: B 280 LEU cc_start: 0.9009 (tt) cc_final: 0.8627 (tt) REVERT: B 298 MET cc_start: 0.9219 (ttt) cc_final: 0.8907 (ttt) REVERT: B 318 GLU cc_start: 0.9480 (tp30) cc_final: 0.9278 (tp30) REVERT: B 326 ASP cc_start: 0.9151 (t70) cc_final: 0.8788 (t0) REVERT: B 329 LEU cc_start: 0.9565 (mt) cc_final: 0.9276 (mt) REVERT: B 543 TRP cc_start: 0.8832 (t60) cc_final: 0.8541 (t60) REVERT: B 544 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 552 MET cc_start: 0.9716 (pmm) cc_final: 0.9511 (ppp) REVERT: B 622 MET cc_start: 0.8791 (ttt) cc_final: 0.8437 (ttt) REVERT: B 629 MET cc_start: 0.7992 (ppp) cc_final: 0.6403 (ppp) REVERT: C 204 LEU cc_start: 0.9517 (tp) cc_final: 0.9275 (tt) REVERT: C 217 GLU cc_start: 0.9566 (tt0) cc_final: 0.8867 (tm-30) REVERT: C 281 HIS cc_start: 0.7434 (p-80) cc_final: 0.6071 (p-80) REVERT: C 326 ASP cc_start: 0.8843 (t70) cc_final: 0.8410 (t0) REVERT: C 329 LEU cc_start: 0.9465 (mt) cc_final: 0.8950 (mt) REVERT: C 552 MET cc_start: 0.9490 (ppp) cc_final: 0.9264 (ppp) REVERT: C 629 MET cc_start: 0.7844 (ppp) cc_final: 0.6151 (ppp) REVERT: C 753 PHE cc_start: 0.8775 (t80) cc_final: 0.8457 (t80) REVERT: C 826 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8397 (tt0) REVERT: D 311 VAL cc_start: 0.9715 (p) cc_final: 0.9505 (m) REVERT: D 317 ASP cc_start: 0.9347 (m-30) cc_final: 0.8815 (p0) REVERT: D 333 PHE cc_start: 0.9347 (m-80) cc_final: 0.8885 (m-80) REVERT: D 562 MET cc_start: 0.8538 (tpt) cc_final: 0.8102 (tpp) REVERT: D 753 PHE cc_start: 0.8351 (t80) cc_final: 0.7982 (t80) REVERT: E 318 GLU cc_start: 0.9665 (mp0) cc_final: 0.9421 (mp0) REVERT: E 321 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8980 (pp30) REVERT: E 376 LEU cc_start: 0.9512 (mt) cc_final: 0.9192 (pp) REVERT: E 629 MET cc_start: 0.8581 (ttm) cc_final: 0.8078 (tmm) REVERT: E 634 MET cc_start: 0.8844 (mmp) cc_final: 0.8516 (mmm) REVERT: E 709 PHE cc_start: 0.9168 (m-10) cc_final: 0.8843 (m-80) REVERT: E 737 MET cc_start: 0.6776 (mmt) cc_final: 0.5941 (mmt) REVERT: F 297 ASN cc_start: 0.8663 (m-40) cc_final: 0.8460 (m-40) REVERT: F 602 LEU cc_start: 0.9630 (pt) cc_final: 0.9429 (pt) REVERT: F 629 MET cc_start: 0.8189 (mmm) cc_final: 0.7185 (tpp) REVERT: F 661 TYR cc_start: 0.9474 (t80) cc_final: 0.9223 (t80) REVERT: F 737 MET cc_start: 0.8352 (mtt) cc_final: 0.7559 (mmm) outliers start: 3 outliers final: 0 residues processed: 395 average time/residue: 0.2007 time to fit residues: 123.9223 Evaluate side-chains 307 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 321 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 203 optimal weight: 0.0470 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 794 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 692 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 849 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN D 747 HIS D 849 ASN E 321 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 564 GLN F 620 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.037480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.027480 restraints weight = 298850.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.028286 restraints weight = 218279.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028913 restraints weight = 171426.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.029398 restraints weight = 141998.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.029801 restraints weight = 121542.903| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29279 Z= 0.193 Angle : 0.694 11.871 39555 Z= 0.353 Chirality : 0.044 0.219 4473 Planarity : 0.005 0.061 5164 Dihedral : 8.198 119.432 4094 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3578 helix: -0.06 (0.11), residues: 2002 sheet: -2.28 (0.25), residues: 389 loop : -1.60 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 379 TYR 0.020 0.002 TYR B 322 PHE 0.022 0.002 PHE F 729 TRP 0.013 0.002 TRP E 543 HIS 0.007 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (29269) covalent geometry : angle 0.69382 / 0.35 (39555) hydrogen bonds : bond 0.04734 / 3.18 ( 1438) hydrogen bonds : angle 5.68185 / 4.05 ( 4245) Misc. bond : bond 0.00267 / 0.12 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 350 time to evaluate : 1.193 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: 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 293 MET cc_start: -0.1139 (tpt) cc_final: -0.1385 (tpp) REVERT: A 333 PHE cc_start: 0.9739 (m-80) cc_final: 0.9328 (m-10) REVERT: B 298 MET cc_start: 0.9221 (ttt) cc_final: 0.8995 (ttt) REVERT: B 310 CYS cc_start: 0.9633 (t) cc_final: 0.9432 (t) REVERT: B 326 ASP cc_start: 0.9284 (t70) cc_final: 0.8841 (t0) REVERT: B 543 TRP cc_start: 0.8971 (t60) cc_final: 0.8740 (t60) REVERT: B 551 MET cc_start: 0.8845 (tpt) cc_final: 0.8582 (tpp) REVERT: B 552 MET cc_start: 0.9760 (pmm) cc_final: 0.9559 (ppp) REVERT: B 622 MET cc_start: 0.8925 (ttt) cc_final: 0.8563 (ttt) REVERT: B 629 MET cc_start: 0.8093 (ppp) cc_final: 0.6639 (ppp) REVERT: C 194 LEU cc_start: 0.9677 (tp) cc_final: 0.9408 (pp) REVERT: C 217 GLU cc_start: 0.9459 (tt0) cc_final: 0.8704 (tm-30) REVERT: C 241 ASP cc_start: 0.9357 (t0) cc_final: 0.9098 (t0) REVERT: C 326 ASP cc_start: 0.9148 (t70) cc_final: 0.8692 (t0) REVERT: C 329 LEU cc_start: 0.9574 (mt) cc_final: 0.9140 (mt) REVERT: C 333 PHE cc_start: 0.9318 (m-80) cc_final: 0.9050 (m-80) REVERT: C 403 MET cc_start: 0.9521 (ptp) cc_final: 0.9147 (ptm) REVERT: C 535 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8889 (mt-10) REVERT: C 536 ILE cc_start: 0.9198 (tp) cc_final: 0.8750 (pt) REVERT: C 552 MET cc_start: 0.9478 (ppp) cc_final: 0.9196 (ppp) REVERT: C 742 LEU cc_start: 0.9365 (mp) cc_final: 0.9112 (pp) REVERT: D 278 ASP cc_start: 0.9290 (p0) cc_final: 0.8990 (t0) REVERT: D 317 ASP cc_start: 0.9309 (m-30) cc_final: 0.8556 (t0) REVERT: D 333 PHE cc_start: 0.9187 (m-80) cc_final: 0.8836 (m-80) REVERT: D 661 TYR cc_start: 0.8922 (t80) cc_final: 0.8616 (t80) REVERT: D 737 MET cc_start: 0.8808 (mtt) cc_final: 0.8120 (mmt) REVERT: D 753 PHE cc_start: 0.8655 (t80) cc_final: 0.8364 (t80) REVERT: E 298 MET cc_start: 0.8996 (ttt) cc_final: 0.8612 (ttt) REVERT: E 376 LEU cc_start: 0.9519 (mt) cc_final: 0.9182 (pp) REVERT: E 626 ASP cc_start: 0.9306 (m-30) cc_final: 0.8986 (m-30) REVERT: E 627 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8970 (pm20) REVERT: E 634 MET cc_start: 0.9426 (mmp) cc_final: 0.9104 (mmm) REVERT: E 709 PHE cc_start: 0.9392 (m-10) cc_final: 0.9027 (m-80) REVERT: E 737 MET cc_start: 0.6882 (mmt) cc_final: 0.6325 (mmp) REVERT: F 297 ASN cc_start: 0.8889 (m-40) cc_final: 0.8550 (t0) REVERT: F 384 ARG cc_start: 0.9274 (mtt-85) cc_final: 0.9007 (mmm160) REVERT: F 392 ASP cc_start: 0.9308 (m-30) cc_final: 0.9098 (m-30) REVERT: F 403 MET cc_start: 0.9033 (tpt) cc_final: 0.8519 (mtm) REVERT: F 629 MET cc_start: 0.8332 (mmm) cc_final: 0.7933 (tpp) REVERT: F 636 GLU cc_start: 0.9372 (mp0) cc_final: 0.9075 (mp0) REVERT: F 661 TYR cc_start: 0.9439 (t80) cc_final: 0.9190 (t80) REVERT: F 737 MET cc_start: 0.8236 (mtt) cc_final: 0.7596 (mmm) outliers start: 2 outliers final: 1 residues processed: 351 average time/residue: 0.1957 time to fit residues: 109.6725 Evaluate side-chains 260 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 354 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 250 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 317 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 692 GLN B 747 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.026952 restraints weight = 305635.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.027724 restraints weight = 223637.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028342 restraints weight = 176361.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028832 restraints weight = 145247.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.029218 restraints weight = 124096.958| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29279 Z= 0.173 Angle : 0.653 9.794 39555 Z= 0.332 Chirality : 0.043 0.159 4473 Planarity : 0.005 0.055 5164 Dihedral : 7.993 120.337 4094 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3578 helix: 0.22 (0.12), residues: 2005 sheet: -2.21 (0.25), residues: 397 loop : -1.44 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 781 TYR 0.013 0.001 TYR B 357 PHE 0.020 0.002 PHE B 687 TRP 0.009 0.001 TRP F 543 HIS 0.005 0.001 HIS F 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (29269) covalent geometry : angle 0.65294 / 0.33 (39555) hydrogen bonds : bond 0.04473 / 2.99 ( 1438) hydrogen bonds : angle 5.58086 / 3.97 ( 4245) Misc. bond : bond 0.00224 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.890 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: 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 293 MET cc_start: -0.0446 (tpt) cc_final: -0.0813 (tpp) REVERT: A 333 PHE cc_start: 0.9744 (m-80) cc_final: 0.9266 (m-80) REVERT: A 403 MET cc_start: 0.8692 (mtt) cc_final: 0.8485 (mtt) REVERT: B 298 MET cc_start: 0.9286 (ttt) cc_final: 0.9000 (ttt) REVERT: B 326 ASP cc_start: 0.9187 (t70) cc_final: 0.8823 (t0) REVERT: B 543 TRP cc_start: 0.9014 (t60) cc_final: 0.8773 (t60) REVERT: B 551 MET cc_start: 0.8730 (tpt) cc_final: 0.8516 (tpp) REVERT: B 622 MET cc_start: 0.8938 (ttt) cc_final: 0.8566 (ttt) REVERT: B 629 MET cc_start: 0.8323 (ppp) cc_final: 0.7153 (ppp) REVERT: C 194 LEU cc_start: 0.9674 (tp) cc_final: 0.9467 (pp) REVERT: C 204 LEU cc_start: 0.9623 (tp) cc_final: 0.9289 (tt) REVERT: C 217 GLU cc_start: 0.9433 (tt0) cc_final: 0.8734 (tm-30) REVERT: C 293 MET cc_start: 0.7138 (mmt) cc_final: 0.6818 (mmm) REVERT: C 298 MET cc_start: 0.8976 (mtp) cc_final: 0.8686 (mtp) REVERT: C 326 ASP cc_start: 0.9234 (t70) cc_final: 0.8860 (t0) REVERT: C 329 LEU cc_start: 0.9580 (mt) cc_final: 0.9130 (mt) REVERT: C 333 PHE cc_start: 0.9385 (m-80) cc_final: 0.8934 (m-80) REVERT: C 535 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8920 (mt-10) REVERT: C 552 MET cc_start: 0.9513 (ppp) cc_final: 0.9259 (ppp) REVERT: C 629 MET cc_start: 0.8617 (ppp) cc_final: 0.7969 (ppp) REVERT: D 242 MET cc_start: 0.8451 (mtp) cc_final: 0.8242 (mtp) REVERT: D 278 ASP cc_start: 0.9348 (p0) cc_final: 0.9124 (t0) REVERT: D 298 MET cc_start: 0.9140 (ttm) cc_final: 0.8674 (ttm) REVERT: D 317 ASP cc_start: 0.9352 (m-30) cc_final: 0.8747 (p0) REVERT: D 333 PHE cc_start: 0.9253 (m-80) cc_final: 0.8845 (m-80) REVERT: D 661 TYR cc_start: 0.9007 (t80) cc_final: 0.8738 (t80) REVERT: D 753 PHE cc_start: 0.8710 (t80) cc_final: 0.8364 (t80) REVERT: E 298 MET cc_start: 0.9030 (ttt) cc_final: 0.8619 (ttt) REVERT: E 626 ASP cc_start: 0.9196 (m-30) cc_final: 0.8946 (m-30) REVERT: E 627 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8913 (pm20) REVERT: E 634 MET cc_start: 0.9596 (mmp) cc_final: 0.9301 (mmm) REVERT: E 699 LEU cc_start: 0.9193 (tp) cc_final: 0.8948 (tp) REVERT: E 709 PHE cc_start: 0.9452 (m-10) cc_final: 0.9040 (m-80) REVERT: E 737 MET cc_start: 0.6833 (mmt) cc_final: 0.6275 (mmm) REVERT: F 297 ASN cc_start: 0.8786 (m-40) cc_final: 0.8432 (t0) REVERT: F 384 ARG cc_start: 0.9301 (mtt-85) cc_final: 0.9086 (mmm160) REVERT: F 392 ASP cc_start: 0.9311 (m-30) cc_final: 0.9077 (m-30) REVERT: F 622 MET cc_start: 0.9215 (ttm) cc_final: 0.8707 (ptm) REVERT: F 629 MET cc_start: 0.8709 (mmm) cc_final: 0.7992 (tpp) REVERT: F 638 MET cc_start: 0.9027 (mmp) cc_final: 0.8599 (mmm) REVERT: F 661 TYR cc_start: 0.9446 (t80) cc_final: 0.9162 (t80) REVERT: F 737 MET cc_start: 0.8323 (mtt) cc_final: 0.7763 (mmm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1987 time to fit residues: 98.1736 Evaluate side-chains 237 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 160 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 427 GLN D 688 ASN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 849 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027026 restraints weight = 311953.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.027835 restraints weight = 222826.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.028467 restraints weight = 171803.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.028953 restraints weight = 139933.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029322 restraints weight = 118931.677| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29279 Z= 0.189 Angle : 0.666 10.630 39555 Z= 0.338 Chirality : 0.043 0.252 4473 Planarity : 0.005 0.080 5164 Dihedral : 7.864 120.636 4094 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3578 helix: 0.40 (0.12), residues: 2008 sheet: -2.07 (0.25), residues: 410 loop : -1.21 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 781 TYR 0.026 0.001 TYR A 322 PHE 0.020 0.002 PHE E 637 TRP 0.010 0.001 TRP F 543 HIS 0.009 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (29269) covalent geometry : angle 0.66558 / 0.34 (39555) hydrogen bonds : bond 0.04384 / 2.94 ( 1438) hydrogen bonds : angle 5.54144 / 3.94 ( 4245) Misc. bond : bond 0.00219 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.0091 (tpt) cc_final: -0.0260 (tpp) REVERT: A 333 PHE cc_start: 0.9722 (m-80) cc_final: 0.9203 (m-80) REVERT: B 293 MET cc_start: 0.6923 (tpp) cc_final: 0.6233 (tpp) REVERT: B 298 MET cc_start: 0.9424 (ttt) cc_final: 0.9106 (ttt) REVERT: B 326 ASP cc_start: 0.9280 (t70) cc_final: 0.8857 (t0) REVERT: B 376 LEU cc_start: 0.9613 (mt) cc_final: 0.9382 (pp) REVERT: B 543 TRP cc_start: 0.9043 (t60) cc_final: 0.8820 (t60) REVERT: B 622 MET cc_start: 0.8928 (ttt) cc_final: 0.8682 (ttt) REVERT: B 629 MET cc_start: 0.8681 (ppp) cc_final: 0.7499 (ppp) REVERT: B 716 MET cc_start: 0.9328 (tpt) cc_final: 0.9127 (tpt) REVERT: C 217 GLU cc_start: 0.9431 (tt0) cc_final: 0.8856 (tt0) REVERT: C 298 MET cc_start: 0.9132 (mtp) cc_final: 0.8726 (mtp) REVERT: C 326 ASP cc_start: 0.9297 (t70) cc_final: 0.9002 (t0) REVERT: C 329 LEU cc_start: 0.9618 (mt) cc_final: 0.9237 (mt) REVERT: C 333 PHE cc_start: 0.9410 (m-80) cc_final: 0.8925 (m-80) REVERT: C 536 ILE cc_start: 0.9263 (tp) cc_final: 0.8905 (pt) REVERT: C 629 MET cc_start: 0.8701 (ppp) cc_final: 0.8048 (ppp) REVERT: C 825 ILE cc_start: 0.9579 (mp) cc_final: 0.9272 (mp) REVERT: D 298 MET cc_start: 0.9137 (ttm) cc_final: 0.8903 (ttm) REVERT: D 317 ASP cc_start: 0.9388 (m-30) cc_final: 0.8800 (p0) REVERT: D 333 PHE cc_start: 0.9217 (m-80) cc_final: 0.8901 (m-80) REVERT: D 661 TYR cc_start: 0.9054 (t80) cc_final: 0.8850 (t80) REVERT: D 737 MET cc_start: 0.8840 (mtt) cc_final: 0.8279 (mmt) REVERT: D 753 PHE cc_start: 0.8829 (t80) cc_final: 0.8531 (t80) REVERT: E 194 LEU cc_start: 0.9829 (tt) cc_final: 0.9619 (mt) REVERT: E 207 GLU cc_start: 0.9576 (mp0) cc_final: 0.9369 (mp0) REVERT: E 298 MET cc_start: 0.9064 (ttt) cc_final: 0.8657 (ttt) REVERT: E 634 MET cc_start: 0.9407 (mmp) cc_final: 0.9178 (mmm) REVERT: E 699 LEU cc_start: 0.9273 (tp) cc_final: 0.9066 (tp) REVERT: E 709 PHE cc_start: 0.9511 (m-10) cc_final: 0.9046 (m-80) REVERT: E 716 MET cc_start: 0.9588 (pmm) cc_final: 0.9308 (pmm) REVERT: E 737 MET cc_start: 0.7164 (mmt) cc_final: 0.6659 (mmm) REVERT: F 297 ASN cc_start: 0.8876 (m-40) cc_final: 0.8531 (t0) REVERT: F 403 MET cc_start: 0.9159 (tpt) cc_final: 0.8592 (ttm) REVERT: F 622 MET cc_start: 0.9261 (ttm) cc_final: 0.8724 (ptm) REVERT: F 629 MET cc_start: 0.8841 (mmm) cc_final: 0.8243 (tpp) REVERT: F 638 MET cc_start: 0.8887 (mmp) cc_final: 0.8293 (mmm) REVERT: F 661 TYR cc_start: 0.9456 (t80) cc_final: 0.9166 (t80) REVERT: F 716 MET cc_start: 0.9610 (ppp) cc_final: 0.9310 (tmm) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.2023 time to fit residues: 93.1834 Evaluate side-chains 220 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 91 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 171 optimal weight: 0.0370 chunk 257 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 GLN E 361 HIS ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 770 HIS F 849 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.027835 restraints weight = 303170.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028670 restraints weight = 213442.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029324 restraints weight = 163469.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.029836 restraints weight = 132187.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.030231 restraints weight = 111225.745| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29279 Z= 0.139 Angle : 0.616 9.858 39555 Z= 0.310 Chirality : 0.043 0.293 4473 Planarity : 0.005 0.050 5164 Dihedral : 7.693 118.787 4094 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3578 helix: 0.61 (0.12), residues: 2010 sheet: -1.93 (0.25), residues: 389 loop : -1.10 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 418 TYR 0.021 0.001 TYR D 656 PHE 0.015 0.002 PHE D 729 TRP 0.025 0.002 TRP A 543 HIS 0.010 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (29269) covalent geometry : angle 0.61630 / 0.31 (39555) hydrogen bonds : bond 0.04130 / 2.79 ( 1438) hydrogen bonds : angle 5.38618 / 3.82 ( 4245) Misc. bond : bond 0.00225 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.156 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: -0.0062 (tpt) cc_final: -0.0603 (tpp) REVERT: A 333 PHE cc_start: 0.9710 (m-80) cc_final: 0.9230 (m-80) REVERT: B 280 LEU cc_start: 0.9442 (mp) cc_final: 0.9231 (mp) REVERT: B 293 MET cc_start: 0.7135 (tpp) cc_final: 0.6612 (tpp) REVERT: B 298 MET cc_start: 0.9422 (ttt) cc_final: 0.9145 (ttt) REVERT: B 376 LEU cc_start: 0.9625 (mt) cc_final: 0.9403 (pp) REVERT: B 535 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8954 (tt0) REVERT: B 543 TRP cc_start: 0.9033 (t60) cc_final: 0.8770 (t60) REVERT: B 622 MET cc_start: 0.8917 (ttt) cc_final: 0.8625 (ttt) REVERT: B 629 MET cc_start: 0.8554 (ppp) cc_final: 0.7465 (ppp) REVERT: C 217 GLU cc_start: 0.9437 (tt0) cc_final: 0.8784 (tt0) REVERT: C 298 MET cc_start: 0.9061 (mtp) cc_final: 0.8743 (mtp) REVERT: C 326 ASP cc_start: 0.9372 (t70) cc_final: 0.9071 (t0) REVERT: C 329 LEU cc_start: 0.9632 (mt) cc_final: 0.9286 (mt) REVERT: C 333 PHE cc_start: 0.9445 (m-80) cc_final: 0.8890 (m-80) REVERT: C 536 ILE cc_start: 0.9300 (tp) cc_final: 0.8963 (pt) REVERT: C 552 MET cc_start: 0.9496 (ppp) cc_final: 0.9236 (ppp) REVERT: C 629 MET cc_start: 0.8680 (ppp) cc_final: 0.7103 (ppp) REVERT: D 317 ASP cc_start: 0.9353 (m-30) cc_final: 0.8775 (p0) REVERT: D 333 PHE cc_start: 0.9203 (m-80) cc_final: 0.8976 (m-80) REVERT: D 737 MET cc_start: 0.8860 (mtt) cc_final: 0.8350 (mmt) REVERT: E 207 GLU cc_start: 0.9552 (mp0) cc_final: 0.9335 (mp0) REVERT: E 298 MET cc_start: 0.9032 (ttt) cc_final: 0.8618 (ttt) REVERT: E 417 ARG cc_start: 0.9158 (mmt180) cc_final: 0.8505 (mmm160) REVERT: E 699 LEU cc_start: 0.9306 (tp) cc_final: 0.9092 (tp) REVERT: E 709 PHE cc_start: 0.9530 (m-10) cc_final: 0.9030 (m-80) REVERT: E 716 MET cc_start: 0.9579 (pmm) cc_final: 0.9070 (pmm) REVERT: F 297 ASN cc_start: 0.8805 (m-40) cc_final: 0.8507 (t0) REVERT: F 403 MET cc_start: 0.9041 (tpt) cc_final: 0.8544 (ttm) REVERT: F 622 MET cc_start: 0.9228 (ttm) cc_final: 0.8691 (ptm) REVERT: F 629 MET cc_start: 0.8712 (mmm) cc_final: 0.8312 (tpp) REVERT: F 638 MET cc_start: 0.8863 (mmp) cc_final: 0.8241 (mmm) REVERT: F 661 TYR cc_start: 0.9442 (t80) cc_final: 0.9133 (t80) REVERT: F 693 VAL cc_start: 0.9649 (t) cc_final: 0.9403 (t) REVERT: F 716 MET cc_start: 0.9634 (ppp) cc_final: 0.9405 (tmm) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1955 time to fit residues: 88.7381 Evaluate side-chains 212 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 171 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 849 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.026527 restraints weight = 307634.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.027300 restraints weight = 225809.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.027919 restraints weight = 178244.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.028407 restraints weight = 146958.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.028795 restraints weight = 125930.605| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29279 Z= 0.134 Angle : 0.603 9.277 39555 Z= 0.304 Chirality : 0.043 0.211 4473 Planarity : 0.004 0.050 5164 Dihedral : 7.538 117.840 4094 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3578 helix: 0.72 (0.12), residues: 2033 sheet: -1.80 (0.25), residues: 396 loop : -1.07 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 332 TYR 0.014 0.001 TYR D 656 PHE 0.013 0.002 PHE E 621 TRP 0.014 0.001 TRP A 543 HIS 0.012 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (29269) covalent geometry : angle 0.60310 / 0.30 (39555) hydrogen bonds : bond 0.03994 / 2.69 ( 1438) hydrogen bonds : angle 5.30807 / 3.76 ( 4245) Misc. bond : bond 0.00220 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.445 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: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: -0.0187 (tpt) cc_final: -0.0656 (tpp) REVERT: A 333 PHE cc_start: 0.9710 (m-80) cc_final: 0.9224 (m-80) REVERT: B 293 MET cc_start: 0.7268 (tpp) cc_final: 0.6641 (tpp) REVERT: B 298 MET cc_start: 0.9434 (ttt) cc_final: 0.9166 (ttt) REVERT: B 376 LEU cc_start: 0.9637 (mt) cc_final: 0.9426 (pp) REVERT: B 535 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8941 (tt0) REVERT: B 543 TRP cc_start: 0.9033 (t60) cc_final: 0.8765 (t60) REVERT: B 622 MET cc_start: 0.8928 (ttt) cc_final: 0.8591 (ttt) REVERT: B 629 MET cc_start: 0.8561 (ppp) cc_final: 0.7497 (ppp) REVERT: C 217 GLU cc_start: 0.9451 (tt0) cc_final: 0.8820 (tt0) REVERT: C 298 MET cc_start: 0.9019 (mtp) cc_final: 0.8760 (mtp) REVERT: C 326 ASP cc_start: 0.9343 (t70) cc_final: 0.9076 (t0) REVERT: C 329 LEU cc_start: 0.9644 (mt) cc_final: 0.9253 (mt) REVERT: C 333 PHE cc_start: 0.9429 (m-80) cc_final: 0.9059 (m-80) REVERT: C 535 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8982 (mt-10) REVERT: C 536 ILE cc_start: 0.9317 (tp) cc_final: 0.8946 (pt) REVERT: C 629 MET cc_start: 0.8705 (ppp) cc_final: 0.7150 (ppp) REVERT: D 242 MET cc_start: 0.8598 (ptp) cc_final: 0.6699 (ptm) REVERT: D 317 ASP cc_start: 0.9337 (m-30) cc_final: 0.8713 (p0) REVERT: D 562 MET cc_start: 0.9417 (tpp) cc_final: 0.9214 (tpp) REVERT: D 737 MET cc_start: 0.8885 (mtt) cc_final: 0.8417 (mmt) REVERT: E 298 MET cc_start: 0.9106 (ttt) cc_final: 0.8714 (ttt) REVERT: E 417 ARG cc_start: 0.9176 (mmt180) cc_final: 0.8538 (mmm160) REVERT: E 622 MET cc_start: 0.9532 (mtm) cc_final: 0.9210 (ptp) REVERT: E 634 MET cc_start: 0.9364 (mmp) cc_final: 0.9148 (mmm) REVERT: E 640 LYS cc_start: 0.9562 (pptt) cc_final: 0.9170 (pptt) REVERT: E 691 LEU cc_start: 0.9716 (tp) cc_final: 0.9420 (mt) REVERT: E 709 PHE cc_start: 0.9559 (m-10) cc_final: 0.9079 (m-80) REVERT: E 716 MET cc_start: 0.9511 (pmm) cc_final: 0.8755 (pmm) REVERT: E 737 MET cc_start: 0.8157 (mmp) cc_final: 0.7661 (mmm) REVERT: F 297 ASN cc_start: 0.8817 (m-40) cc_final: 0.8493 (t0) REVERT: F 403 MET cc_start: 0.9006 (tpt) cc_final: 0.8508 (ttm) REVERT: F 622 MET cc_start: 0.9256 (ttm) cc_final: 0.8721 (ptm) REVERT: F 629 MET cc_start: 0.8736 (mmm) cc_final: 0.8339 (tpp) REVERT: F 638 MET cc_start: 0.8801 (mmp) cc_final: 0.8097 (mmm) REVERT: F 661 TYR cc_start: 0.9455 (t80) cc_final: 0.9147 (t80) REVERT: F 716 MET cc_start: 0.9654 (ppp) cc_final: 0.9300 (tmm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1970 time to fit residues: 87.2889 Evaluate side-chains 210 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 242 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 7 optimal weight: 0.0010 chunk 132 optimal weight: 2.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS B 794 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.039717 restraints weight = 272846.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.040287 restraints weight = 213773.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.040659 restraints weight = 180063.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.041002 restraints weight = 159539.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041202 restraints weight = 146075.154| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29279 Z= 0.166 Angle : 0.629 9.780 39555 Z= 0.320 Chirality : 0.043 0.266 4473 Planarity : 0.005 0.050 5164 Dihedral : 7.449 119.255 4094 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3578 helix: 0.71 (0.12), residues: 2049 sheet: -1.66 (0.26), residues: 403 loop : -0.93 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 331 TYR 0.015 0.001 TYR D 656 PHE 0.014 0.002 PHE D 729 TRP 0.008 0.001 TRP A 543 HIS 0.020 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (29269) covalent geometry : angle 0.62905 / 0.32 (39555) hydrogen bonds : bond 0.04091 / 2.76 ( 1438) hydrogen bonds : angle 5.31935 / 3.78 ( 4245) Misc. bond : bond 0.00213 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.168 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 293 MET cc_start: -0.0284 (tpt) cc_final: -0.1327 (mmt) REVERT: A 333 PHE cc_start: 0.9713 (m-80) cc_final: 0.9269 (m-80) REVERT: A 403 MET cc_start: 0.8611 (mtt) cc_final: 0.8409 (mtt) REVERT: B 293 MET cc_start: 0.7251 (tpp) cc_final: 0.6699 (tpp) REVERT: B 298 MET cc_start: 0.9516 (ttt) cc_final: 0.9278 (ttt) REVERT: B 622 MET cc_start: 0.8879 (ttt) cc_final: 0.8608 (ttt) REVERT: B 629 MET cc_start: 0.8737 (ppp) cc_final: 0.7711 (ppp) REVERT: C 217 GLU cc_start: 0.9447 (tt0) cc_final: 0.8844 (tt0) REVERT: C 298 MET cc_start: 0.9095 (mtp) cc_final: 0.8855 (mtp) REVERT: C 326 ASP cc_start: 0.9421 (t70) cc_final: 0.9146 (t0) REVERT: C 329 LEU cc_start: 0.9700 (mt) cc_final: 0.9325 (mt) REVERT: C 333 PHE cc_start: 0.9462 (m-80) cc_final: 0.9067 (m-80) REVERT: C 535 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9038 (mt-10) REVERT: C 536 ILE cc_start: 0.9400 (tp) cc_final: 0.9046 (pt) REVERT: C 629 MET cc_start: 0.8860 (ppp) cc_final: 0.7406 (ppp) REVERT: D 317 ASP cc_start: 0.9430 (m-30) cc_final: 0.8831 (p0) REVERT: D 322 TYR cc_start: 0.9232 (m-80) cc_final: 0.8941 (m-10) REVERT: D 333 PHE cc_start: 0.9192 (m-80) cc_final: 0.8858 (m-80) REVERT: D 737 MET cc_start: 0.8965 (mtt) cc_final: 0.8494 (mmt) REVERT: E 298 MET cc_start: 0.9256 (ttt) cc_final: 0.8895 (ttt) REVERT: E 417 ARG cc_start: 0.9180 (mmt180) cc_final: 0.8541 (mmm160) REVERT: E 622 MET cc_start: 0.9561 (mtm) cc_final: 0.9319 (mtm) REVERT: E 634 MET cc_start: 0.9640 (mmp) cc_final: 0.9356 (mmm) REVERT: E 716 MET cc_start: 0.9508 (pmm) cc_final: 0.8554 (pmm) REVERT: E 737 MET cc_start: 0.8219 (mmp) cc_final: 0.7902 (mmm) REVERT: F 297 ASN cc_start: 0.8890 (m-40) cc_final: 0.8675 (t0) REVERT: F 622 MET cc_start: 0.9307 (ttm) cc_final: 0.8752 (ptm) REVERT: F 629 MET cc_start: 0.9167 (mmm) cc_final: 0.8892 (tpp) REVERT: F 638 MET cc_start: 0.9060 (mmp) cc_final: 0.8274 (mmm) REVERT: F 716 MET cc_start: 0.9740 (ppp) cc_final: 0.9298 (tmm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1853 time to fit residues: 77.9958 Evaluate side-chains 187 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 227 optimal weight: 0.0970 chunk 54 optimal weight: 0.0870 chunk 216 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 3 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.0538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN D 174 GLN D 201 ASN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.026582 restraints weight = 303891.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027372 restraints weight = 221570.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.028005 restraints weight = 173441.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.028484 restraints weight = 142884.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.028877 restraints weight = 122466.223| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29279 Z= 0.116 Angle : 0.606 9.110 39555 Z= 0.302 Chirality : 0.043 0.197 4473 Planarity : 0.004 0.065 5164 Dihedral : 7.248 116.324 4094 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3578 helix: 0.85 (0.12), residues: 2033 sheet: -1.56 (0.27), residues: 374 loop : -0.89 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 320 TYR 0.017 0.001 TYR C 380 PHE 0.029 0.002 PHE B 687 TRP 0.018 0.001 TRP B 543 HIS 0.016 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (29269) covalent geometry : angle 0.60630 / 0.30 (39555) hydrogen bonds : bond 0.03815 / 2.58 ( 1438) hydrogen bonds : angle 5.20556 / 3.68 ( 4245) Misc. bond : bond 0.00228 / 0.11 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.116 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: A 293 MET cc_start: 0.0100 (tpt) cc_final: -0.1088 (mmt) REVERT: A 333 PHE cc_start: 0.9665 (m-80) cc_final: 0.9206 (m-80) REVERT: B 278 ASP cc_start: 0.9511 (p0) cc_final: 0.9170 (t0) REVERT: B 293 MET cc_start: 0.7290 (tpp) cc_final: 0.6607 (tpp) REVERT: B 298 MET cc_start: 0.9459 (ttt) cc_final: 0.9229 (ttt) REVERT: B 535 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9071 (tt0) REVERT: B 543 TRP cc_start: 0.8985 (t60) cc_final: 0.8664 (t60) REVERT: B 622 MET cc_start: 0.8913 (ttt) cc_final: 0.8646 (ttt) REVERT: B 629 MET cc_start: 0.8627 (ppp) cc_final: 0.7835 (ppp) REVERT: C 217 GLU cc_start: 0.9446 (tt0) cc_final: 0.8849 (tt0) REVERT: C 326 ASP cc_start: 0.9443 (t70) cc_final: 0.9192 (t0) REVERT: C 329 LEU cc_start: 0.9664 (mt) cc_final: 0.9279 (mt) REVERT: C 333 PHE cc_start: 0.9423 (m-80) cc_final: 0.9065 (m-80) REVERT: C 535 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8988 (mt-10) REVERT: C 536 ILE cc_start: 0.9352 (tp) cc_final: 0.9001 (pt) REVERT: C 629 MET cc_start: 0.8701 (ppp) cc_final: 0.7292 (ppp) REVERT: D 317 ASP cc_start: 0.9374 (m-30) cc_final: 0.8840 (p0) REVERT: D 333 PHE cc_start: 0.9229 (m-80) cc_final: 0.8901 (m-80) REVERT: D 383 ASP cc_start: 0.9325 (m-30) cc_final: 0.9046 (p0) REVERT: D 737 MET cc_start: 0.8967 (mtt) cc_final: 0.8461 (mmt) REVERT: E 298 MET cc_start: 0.9236 (ttt) cc_final: 0.8896 (ttt) REVERT: E 417 ARG cc_start: 0.9172 (mmt180) cc_final: 0.8549 (mmm-85) REVERT: E 622 MET cc_start: 0.9523 (mtm) cc_final: 0.9296 (mtm) REVERT: E 691 LEU cc_start: 0.9773 (tp) cc_final: 0.9412 (mt) REVERT: E 737 MET cc_start: 0.8196 (mmp) cc_final: 0.7477 (mmm) REVERT: F 403 MET cc_start: 0.8970 (tpt) cc_final: 0.8412 (ttm) REVERT: F 622 MET cc_start: 0.9299 (ttm) cc_final: 0.8747 (ptm) REVERT: F 629 MET cc_start: 0.8672 (mmm) cc_final: 0.8287 (tpp) REVERT: F 638 MET cc_start: 0.9199 (mmm) cc_final: 0.8901 (mmm) REVERT: F 716 MET cc_start: 0.9669 (ppp) cc_final: 0.9283 (tmm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1875 time to fit residues: 81.7374 Evaluate side-chains 202 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 92 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 736 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.036031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.026515 restraints weight = 311047.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.027308 restraints weight = 226935.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.027928 restraints weight = 176997.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.028416 restraints weight = 146110.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.028798 restraints weight = 124759.384| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29279 Z= 0.125 Angle : 0.606 8.993 39555 Z= 0.304 Chirality : 0.043 0.226 4473 Planarity : 0.004 0.051 5164 Dihedral : 7.148 116.651 4094 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3578 helix: 0.90 (0.12), residues: 2035 sheet: -1.55 (0.27), residues: 374 loop : -0.76 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 815 TYR 0.012 0.001 TYR D 656 PHE 0.023 0.002 PHE B 687 TRP 0.011 0.001 TRP B 543 HIS 0.003 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (29269) covalent geometry : angle 0.60553 / 0.30 (39555) hydrogen bonds : bond 0.03834 / 2.58 ( 1438) hydrogen bonds : angle 5.17502 / 3.65 ( 4245) Misc. bond : bond 0.00213 / 0.10 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.214 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: A 293 MET cc_start: -0.0565 (tpt) cc_final: -0.1754 (mmt) REVERT: A 333 PHE cc_start: 0.9668 (m-80) cc_final: 0.9238 (m-80) REVERT: A 622 MET cc_start: 0.8813 (ppp) cc_final: 0.8497 (ppp) REVERT: B 278 ASP cc_start: 0.9531 (p0) cc_final: 0.9184 (t0) REVERT: B 293 MET cc_start: 0.7389 (tpp) cc_final: 0.6912 (tpp) REVERT: B 298 MET cc_start: 0.9472 (ttt) cc_final: 0.9248 (ttt) REVERT: B 535 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9072 (tt0) REVERT: B 543 TRP cc_start: 0.9046 (t60) cc_final: 0.8713 (t60) REVERT: B 622 MET cc_start: 0.8943 (ttt) cc_final: 0.8671 (ttt) REVERT: B 629 MET cc_start: 0.8684 (ppp) cc_final: 0.7191 (ppp) REVERT: C 217 GLU cc_start: 0.9437 (tt0) cc_final: 0.8816 (tt0) REVERT: C 326 ASP cc_start: 0.9475 (t70) cc_final: 0.9238 (t0) REVERT: C 329 LEU cc_start: 0.9677 (mt) cc_final: 0.9310 (mt) REVERT: C 333 PHE cc_start: 0.9415 (m-80) cc_final: 0.9030 (m-80) REVERT: C 535 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9006 (mt-10) REVERT: C 536 ILE cc_start: 0.9354 (tp) cc_final: 0.9008 (pt) REVERT: C 629 MET cc_start: 0.8748 (ppp) cc_final: 0.7756 (ppp) REVERT: D 317 ASP cc_start: 0.9461 (m-30) cc_final: 0.8897 (p0) REVERT: D 383 ASP cc_start: 0.9324 (m-30) cc_final: 0.8994 (p0) REVERT: D 626 ASP cc_start: 0.9176 (t0) cc_final: 0.8945 (p0) REVERT: D 737 MET cc_start: 0.8966 (mtt) cc_final: 0.8475 (mmt) REVERT: E 298 MET cc_start: 0.9273 (ttt) cc_final: 0.8952 (ttt) REVERT: E 417 ARG cc_start: 0.9160 (mmt180) cc_final: 0.8582 (mmm-85) REVERT: E 622 MET cc_start: 0.9532 (mtm) cc_final: 0.9302 (mtm) REVERT: E 691 LEU cc_start: 0.9779 (tp) cc_final: 0.9440 (mt) REVERT: E 716 MET cc_start: 0.9530 (pmm) cc_final: 0.9155 (pmm) REVERT: E 737 MET cc_start: 0.8223 (mmp) cc_final: 0.7562 (mmm) REVERT: F 293 MET cc_start: 0.5946 (mmt) cc_final: 0.4861 (tpp) REVERT: F 403 MET cc_start: 0.8964 (tpt) cc_final: 0.8421 (ttm) REVERT: F 622 MET cc_start: 0.9317 (ttm) cc_final: 0.8767 (ptm) REVERT: F 629 MET cc_start: 0.8692 (mmm) cc_final: 0.8311 (tpp) REVERT: F 638 MET cc_start: 0.9211 (mmm) cc_final: 0.8939 (mmm) REVERT: F 716 MET cc_start: 0.9676 (ppp) cc_final: 0.9277 (tmm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1914 time to fit residues: 79.9548 Evaluate side-chains 193 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 188 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 220 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 341 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 263 optimal weight: 0.0030 chunk 267 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 736 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 857 GLN ** F 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026992 restraints weight = 306750.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.027813 restraints weight = 223301.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.028471 restraints weight = 174221.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.028975 restraints weight = 142505.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.029370 restraints weight = 121799.541| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29279 Z= 0.115 Angle : 0.612 8.652 39555 Z= 0.305 Chirality : 0.043 0.184 4473 Planarity : 0.004 0.051 5164 Dihedral : 7.074 115.233 4094 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3578 helix: 0.98 (0.12), residues: 2004 sheet: -1.55 (0.27), residues: 381 loop : -0.71 (0.19), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 171 TYR 0.016 0.001 TYR C 322 PHE 0.019 0.001 PHE B 687 TRP 0.013 0.001 TRP B 543 HIS 0.006 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (29269) covalent geometry : angle 0.61220 / 0.31 (39555) hydrogen bonds : bond 0.03758 / 2.54 ( 1438) hydrogen bonds : angle 5.11913 / 3.61 ( 4245) Misc. bond : bond 0.00222 / 0.11 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.11 seconds wall clock time: 87 minutes 44.44 seconds (5264.44 seconds total)