Starting phenix.real_space_refine on Mon Sep 14 20:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.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 { model { file = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rn4_4942/09_2026/6rn4_4942.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= 0.001 sd= 0.008 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 32 5.49 5 S 126 5.16 5 C 20458 2.51 5 N 5926 2.21 5 O 6291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s 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: 32833 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 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: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5364 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.57, per 1000 atoms: 0.23 Number of scatterers: 32833 At special positions: 0 Unit cell: (141.44, 183.04, 168.48, 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 126 16.00 P 32 15.00 O 6291 8.00 N 5926 7.00 C 20458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7672 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 32 sheets defined 64.4% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.630A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 4.272A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 342 through 361 removed outlier: 4.454A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.601A 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 410 through 430 Processing helix chain 'A' and resid 443 through 493 Processing helix chain 'A' and resid 494 through 524 removed outlier: 3.682A pdb=" N MET A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 561 through 570 removed outlier: 4.158A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 610 through 623 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.865A pdb=" N GLU A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.771A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 734 through 749 Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 814 through 835 Proline residue: A 828 - end of helix Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.737A pdb=" N TYR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.678A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.557A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.658A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 305' Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.632A 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 406 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 443 through 493 Processing helix chain 'B' and resid 494 through 524 removed outlier: 3.968A pdb=" N MET B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.717A 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 633 through 637 removed outlier: 3.696A pdb=" N GLU B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 647 Processing helix chain 'B' and resid 653 through 657 removed outlier: 3.919A pdb=" N TYR B 656 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 653 through 657' Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.617A pdb=" N GLU B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 4.003A 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: 3.837A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.713A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 Proline residue: B 828 - end of helix removed outlier: 3.996A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.764A pdb=" N GLN C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.607A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.635A pdb=" N ALA C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.897A pdb=" N ARG C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.601A pdb=" N THR C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.831A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 443 through 493 Processing helix chain 'C' and resid 494 through 524 removed outlier: 3.947A pdb=" N MET C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix removed outlier: 3.549A pdb=" N MET C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 542 removed outlier: 3.928A pdb=" N ILE C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 561 Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.648A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.794A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 659 " --> pdb=" O TYR C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 659' Processing helix chain 'C' and resid 661 through 669 removed outlier: 3.666A pdb=" N ALA C 665 " --> pdb=" O TYR C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.844A pdb=" N LEU C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 729 Processing helix chain 'C' and resid 733 through 749 removed outlier: 3.873A pdb=" N MET C 737 " --> pdb=" O ASP C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 788 Processing helix chain 'C' and resid 796 through 808 removed outlier: 3.655A pdb=" N LEU C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 808 " --> pdb=" O SER C 804 " (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 160 through 164 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.200A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.287A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.571A pdb=" N TYR D 319 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 361 removed outlier: 3.576A pdb=" N THR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.523A pdb=" N ILE D 391 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 443 through 493 Processing helix chain 'D' and resid 494 through 524 removed outlier: 3.760A pdb=" N MET D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 561 through 567 removed outlier: 3.716A pdb=" N HIS D 567 " --> pdb=" O GLU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.670A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 624 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.819A pdb=" N TYR D 656 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU D 657 " --> pdb=" O VAL D 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 653 through 657' Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.502A pdb=" N ALA D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.793A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.819A 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 684 through 697 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 734 through 749 Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'D' and resid 814 through 834 removed outlier: 3.774A 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 225 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.580A pdb=" N LEU E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 270 removed outlier: 3.659A pdb=" N GLU E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 Processing helix chain 'E' and resid 295 through 304 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 326 through 333 removed outlier: 5.574A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 332 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 362 removed outlier: 3.577A pdb=" N THR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.617A pdb=" N ILE E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 410 through 430 Processing helix chain 'E' and resid 443 through 493 Processing helix chain 'E' and resid 495 through 524 Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 532 through 545 removed outlier: 3.749A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 removed outlier: 3.771A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.790A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 624 removed outlier: 3.607A pdb=" N LEU E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.639A pdb=" N GLY E 659 " --> pdb=" O TYR E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 685 through 696 removed outlier: 4.249A pdb=" N ILE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 734 through 749 Processing helix chain 'E' and resid 750 through 755 removed outlier: 3.772A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 790 removed outlier: 3.950A pdb=" N GLU E 788 " --> pdb=" O LYS E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 807 removed outlier: 3.821A pdb=" N LEU E 800 " --> pdb=" O SER E 796 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS E 801 " --> pdb=" O ASP E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 834 removed outlier: 3.535A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.853A pdb=" N TYR F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 164' Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.859A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 279 through 286 Processing helix chain 'F' and resid 295 through 304 Proline residue: F 301 - end of helix removed outlier: 3.680A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.937A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.700A pdb=" N THR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 406 Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 443 through 493 Processing helix chain 'F' and resid 494 through 524 removed outlier: 3.928A pdb=" N MET F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 566 Processing helix chain 'F' and resid 573 through 590 removed outlier: 3.621A pdb=" N GLY F 590 " --> pdb=" O ARG F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 622 Processing helix chain 'F' and resid 635 through 638 removed outlier: 4.196A pdb=" N MET F 638 " --> pdb=" O SER F 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 635 through 638' Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.559A pdb=" N ARG F 645 " --> pdb=" O HIS F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.563A pdb=" N ALA F 682 " --> pdb=" O VAL F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 696 removed outlier: 3.606A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 750 through 755 Processing helix chain 'F' and resid 768 through 790 Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 813 through 834 Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 3.625A pdb=" N ILE A 166 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 239 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 603 removed outlier: 5.221A pdb=" N GLY A 599 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET A 716 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 601 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.649A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.998A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.373A pdb=" N GLN B 364 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 630 through 631 removed outlier: 6.693A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 717 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLY B 599 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N MET B 716 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 601 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER B 718 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 603 " --> pdb=" O SER B 718 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB2, first strand: chain 'B' and resid 792 through 795 Processing sheet with id=AB3, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.089A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 314 through 315 removed outlier: 7.865A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 364 through 365 removed outlier: 7.320A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 600 through 603 removed outlier: 5.640A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 699 removed outlier: 3.674A pdb=" N VAL C 707 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 793 through 795 removed outlier: 7.006A pdb=" N HIS C 794 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 848 " --> pdb=" O HIS C 794 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.789A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 312 through 313 removed outlier: 3.518A pdb=" N VAL D 336 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 631 through 633 removed outlier: 7.611A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 602 " --> pdb=" O VAL D 761 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 698 through 699 Processing sheet with id=AC4, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.427A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.977A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 312 through 315 removed outlier: 5.908A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.791A pdb=" N GLN E 364 " --> pdb=" O VAL E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.131A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 792 through 795 removed outlier: 6.457A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.864A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 312 through 315 removed outlier: 8.023A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 203 " --> pdb=" O GLN F 334 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.547A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 630 through 633 removed outlier: 3.715A pdb=" N LEU F 675 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 632 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 677 " --> pdb=" O ILE F 632 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE F 601 " --> pdb=" O MET F 716 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER F 718 " --> pdb=" O PHE F 601 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE F 603 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 792 through 795 removed outlier: 6.920A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 843 " --> pdb=" O HIS F 858 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 858 " --> pdb=" O VAL F 843 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1838 hydrogen bonds defined for protein. 5427 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: 8.89 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 5973 1.32 - 1.48: 12611 1.48 - 1.64: 14471 1.64 - 1.80: 183 1.80 - 1.96: 47 Bond restraints: 33285 Sorted by residual: bond pdb=" C GLY B 253 " pdb=" N GLU B 254 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.46e-02 4.69e+03 1.60e+01 bond pdb=" C LEU D 177 " pdb=" N ASP D 178 " ideal model delta sigma weight residual 1.331 1.271 0.061 1.63e-02 3.76e+03 1.39e+01 bond pdb=" CB GLU E 613 " pdb=" CG GLU E 613 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.33e+01 bond pdb=" CB ASP D 388 " pdb=" CG ASP D 388 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.20e+01 ... (remaining 33280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 44845 7.60 - 15.20: 78 15.20 - 22.79: 5 22.79 - 30.39: 0 30.39 - 37.99: 1 Bond angle restraints: 44929 Sorted by residual: angle pdb=" O1B AGS F1001 " pdb=" PB AGS F1001 " pdb=" O2B AGS F1001 " ideal model delta sigma weight residual 112.09 74.10 37.99 4.09e+00 5.99e-02 8.64e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CA PRO F 409 " ideal model delta sigma weight residual 127.00 148.13 -21.13 2.40e+00 1.74e-01 7.75e+01 angle pdb=" N VAL C 686 " pdb=" CA VAL C 686 " pdb=" C VAL C 686 " ideal model delta sigma weight residual 113.22 103.26 9.96 1.23e+00 6.61e-01 6.56e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CD PRO F 409 " ideal model delta sigma weight residual 120.60 103.04 17.56 2.20e+00 2.07e-01 6.37e+01 angle pdb=" N LEU F 444 " pdb=" CA LEU F 444 " pdb=" C LEU F 444 " ideal model delta sigma weight residual 113.50 106.14 7.36 1.23e+00 6.61e-01 3.58e+01 ... (remaining 44924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.66: 20105 27.66 - 55.31: 397 55.31 - 82.97: 26 82.97 - 110.62: 0 110.62 - 138.28: 2 Dihedral angle restraints: 20530 sinusoidal: 8655 harmonic: 11875 Sorted by residual: dihedral pdb=" CA GLY F 608 " pdb=" C GLY F 608 " pdb=" N VAL F 609 " pdb=" CA VAL F 609 " ideal model delta harmonic sigma weight residual -180.00 -131.68 -48.32 0 5.00e+00 4.00e-02 9.34e+01 dihedral pdb=" CA TYR A 656 " pdb=" C TYR A 656 " pdb=" N GLU A 657 " pdb=" CA GLU A 657 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA VAL B 548 " pdb=" C VAL B 548 " pdb=" N SER B 549 " pdb=" CA SER B 549 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 20527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4288 0.085 - 0.171: 749 0.171 - 0.256: 45 0.256 - 0.342: 5 0.342 - 0.427: 1 Chirality restraints: 5088 Sorted by residual: chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.75 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" PA AGS C1001 " pdb=" O2A AGS C1001 " pdb=" O3A AGS C1001 " pdb=" O5' AGS C1001 " both_signs ideal model delta sigma weight residual True 3.18 -2.89 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5085 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 661 " -0.036 2.00e-02 2.50e+03 2.79e-02 1.56e+01 pdb=" CG TYR E 661 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR E 661 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 661 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 661 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 661 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 661 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 661 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 643 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C VAL C 643 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL C 643 " -0.023 2.00e-02 2.50e+03 pdb=" N SER C 644 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 683 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO E 684 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 684 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 684 " 0.045 5.00e-02 4.00e+02 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1259 2.69 - 3.24: 32264 3.24 - 3.79: 54447 3.79 - 4.35: 67768 4.35 - 4.90: 109390 Nonbonded interactions: 265128 Sorted by model distance: nonbonded pdb=" O GLY F 608 " pdb=" O1B AGS F1001 " model vdw 2.132 2.432 nonbonded pdb=" O1B AGS E1001 " pdb=" O2A AGS E1001 " model vdw 2.173 3.040 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.223 3.040 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.225 3.040 nonbonded pdb=" O2A AGS B1001 " pdb=" O2B AGS B1001 " model vdw 2.226 3.040 ... (remaining 265123 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' selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 1001)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 1001)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 1001)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 1001)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 1001)) } 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: 1.520 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: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.210 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 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:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.012 0.185 33304 Z= 0.519 Angle : 1.245 37.988 44929 Z= 0.660 Chirality : 0.062 0.427 5088 Planarity : 0.008 0.084 5869 Dihedral : 10.974 138.276 12858 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.25 % Favored : 90.73 % Rotamer: Outliers : 0.41 % Allowed : 1.28 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.67 (0.11), residues: 4077 helix: -2.01 (0.08), residues: 2332 sheet: -2.84 (0.25), residues: 354 loop : -2.76 (0.14), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 596 TYR 0.068 0.003 TYR E 661 PHE 0.038 0.005 PHE B 709 TRP 0.043 0.005 TRP E 543 HIS 0.018 0.003 HIS F 747 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.52 (33285) covalent geometry : angle 1.24525 / 0.66 (44929) hydrogen bonds : bond 0.14366 / 9.77 ( 1838) hydrogen bonds : angle 7.62748 / 5.32 ( 5427) Misc. bond : bond 0.00849 / 0.52 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1066 time to evaluate : 1.383 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: A 242 MET cc_start: 0.7907 (mmp) cc_final: 0.7433 (mmp) REVERT: A 318 GLU cc_start: 0.8139 (mp0) cc_final: 0.7859 (mp0) REVERT: A 631 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7305 (ttm-80) REVERT: A 645 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7738 (ttm110) REVERT: A 661 TYR cc_start: 0.7165 (t80) cc_final: 0.6848 (t80) REVERT: A 673 VAL cc_start: 0.9093 (t) cc_final: 0.8855 (p) REVERT: A 749 PHE cc_start: 0.7611 (m-10) cc_final: 0.7014 (m-10) REVERT: A 776 GLN cc_start: 0.8851 (mt0) cc_final: 0.8472 (tp40) REVERT: B 163 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8238 (mtmt) REVERT: B 201 ASN cc_start: 0.6804 (m-40) cc_final: 0.6523 (m-40) REVERT: B 265 ASP cc_start: 0.8429 (m-30) cc_final: 0.7798 (m-30) REVERT: B 275 LEU cc_start: 0.9535 (tp) cc_final: 0.9288 (tt) REVERT: B 299 LEU cc_start: 0.9181 (mp) cc_final: 0.8936 (mt) REVERT: B 310 CYS cc_start: 0.7111 (t) cc_final: 0.6484 (t) REVERT: B 430 MET cc_start: 0.3692 (mmm) cc_final: 0.3020 (ttm) REVERT: B 587 SER cc_start: 0.9014 (t) cc_final: 0.8786 (p) REVERT: B 615 CYS cc_start: 0.8367 (m) cc_final: 0.8098 (t) REVERT: B 627 GLU cc_start: 0.7659 (mp0) cc_final: 0.7291 (tm-30) REVERT: B 629 MET cc_start: 0.8030 (ptm) cc_final: 0.7624 (ppp) REVERT: B 634 MET cc_start: 0.8309 (mmm) cc_final: 0.8033 (mmm) REVERT: B 719 ASN cc_start: 0.8199 (p0) cc_final: 0.7885 (m110) REVERT: B 758 ASP cc_start: 0.7426 (t0) cc_final: 0.6848 (m-30) REVERT: B 821 ILE cc_start: 0.8869 (mt) cc_final: 0.8526 (mm) REVERT: B 846 LEU cc_start: 0.9372 (mt) cc_final: 0.9103 (tt) REVERT: C 196 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8017 (mtm-85) REVERT: C 246 VAL cc_start: 0.7622 (t) cc_final: 0.7282 (m) REVERT: C 257 GLU cc_start: 0.8554 (tt0) cc_final: 0.8092 (tm-30) REVERT: C 268 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8499 (tptt) REVERT: C 318 GLU cc_start: 0.8466 (mp0) cc_final: 0.7887 (mp0) REVERT: C 498 MET cc_start: 0.4996 (mmm) cc_final: 0.4714 (mmm) REVERT: C 602 LEU cc_start: 0.8887 (tp) cc_final: 0.8618 (tt) REVERT: C 615 CYS cc_start: 0.9154 (m) cc_final: 0.8361 (t) REVERT: C 638 MET cc_start: 0.8518 (mtm) cc_final: 0.8283 (mtm) REVERT: C 821 ILE cc_start: 0.8299 (mt) cc_final: 0.8098 (mm) REVERT: C 827 ASN cc_start: 0.9264 (m-40) cc_final: 0.8989 (m-40) REVERT: D 180 VAL cc_start: 0.8320 (t) cc_final: 0.8062 (p) REVERT: D 274 ILE cc_start: 0.8103 (mt) cc_final: 0.7782 (mm) REVERT: D 323 ILE cc_start: 0.8089 (mt) cc_final: 0.7882 (mm) REVERT: D 358 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7683 (pp20) REVERT: D 395 ASP cc_start: 0.8768 (t0) cc_final: 0.8269 (t0) REVERT: D 524 MET cc_start: 0.5121 (mmm) cc_final: 0.4588 (mmt) REVERT: D 630 VAL cc_start: 0.8618 (t) cc_final: 0.8312 (t) REVERT: D 691 LEU cc_start: 0.8101 (mt) cc_final: 0.7650 (mt) REVERT: D 760 VAL cc_start: 0.8492 (t) cc_final: 0.8000 (p) REVERT: D 774 ILE cc_start: 0.9058 (mt) cc_final: 0.8716 (tp) REVERT: D 792 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7616 (mp0) REVERT: D 834 LEU cc_start: 0.9041 (mt) cc_final: 0.8770 (mt) REVERT: E 319 TYR cc_start: 0.8508 (t80) cc_final: 0.8218 (t80) REVERT: E 335 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8246 (tptp) REVERT: E 370 ILE cc_start: 0.8177 (mt) cc_final: 0.7900 (mt) REVERT: E 540 LEU cc_start: 0.8636 (tp) cc_final: 0.8419 (tt) REVERT: E 562 MET cc_start: 0.8432 (tpt) cc_final: 0.8181 (tpt) REVERT: E 591 LEU cc_start: 0.8535 (mp) cc_final: 0.8313 (mp) REVERT: E 621 PHE cc_start: 0.8223 (t80) cc_final: 0.7818 (t80) REVERT: E 691 LEU cc_start: 0.8476 (mt) cc_final: 0.7967 (tp) REVERT: E 701 ASP cc_start: 0.8802 (p0) cc_final: 0.8283 (p0) REVERT: E 784 LYS cc_start: 0.9177 (tttt) cc_final: 0.8940 (tmmt) REVERT: E 817 LEU cc_start: 0.8826 (tp) cc_final: 0.8612 (tp) REVERT: F 242 MET cc_start: 0.6249 (mmp) cc_final: 0.5824 (tpp) REVERT: F 319 TYR cc_start: 0.7514 (t80) cc_final: 0.6816 (t80) REVERT: F 322 TYR cc_start: 0.7298 (m-10) cc_final: 0.6909 (m-10) REVERT: F 324 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6164 (pp20) REVERT: F 333 PHE cc_start: 0.7355 (m-80) cc_final: 0.7149 (m-10) REVERT: F 456 SER cc_start: 0.9119 (t) cc_final: 0.8764 (p) REVERT: F 457 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8389 (tm-30) REVERT: F 462 TRP cc_start: 0.7601 (t60) cc_final: 0.6524 (t60) REVERT: F 476 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7156 (tptp) REVERT: F 603 PHE cc_start: 0.7742 (m-10) cc_final: 0.7180 (m-10) REVERT: F 613 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8063 (tt0) REVERT: F 614 LEU cc_start: 0.8421 (tp) cc_final: 0.8087 (mt) REVERT: F 797 ASP cc_start: 0.8109 (m-30) cc_final: 0.7901 (p0) REVERT: F 801 LYS cc_start: 0.9394 (mtpp) cc_final: 0.8953 (mttt) outliers start: 14 outliers final: 3 residues processed: 1079 average time/residue: 0.2300 time to fit residues: 383.8487 Evaluate side-chains 577 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 334 GLN A 362 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 334 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS B 831 GLN B 858 HIS C 192 GLN C 454 GLN C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN C 822 GLN C 849 ASN D 281 HIS D 512 GLN D 641 HIS D 747 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 849 ASN D 858 HIS E 221 GLN E 269 GLN E 297 ASN ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 GLN E 764 HIS E 794 HIS E 822 GLN ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS F 778 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.131172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104465 restraints weight = 102328.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.106885 restraints weight = 69265.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106799 restraints weight = 48296.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.108828 restraints weight = 43314.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.107906 restraints weight = 37265.536| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33304 Z= 0.199 Angle : 0.791 23.491 44929 Z= 0.398 Chirality : 0.045 0.237 5088 Planarity : 0.006 0.084 5869 Dihedral : 8.440 129.538 4638 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 4077 helix: -0.58 (0.10), residues: 2348 sheet: -2.75 (0.25), residues: 346 loop : -2.21 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 785 TYR 0.023 0.002 TYR C 653 PHE 0.018 0.002 PHE C 276 TRP 0.024 0.003 TRP B 543 HIS 0.007 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (33285) covalent geometry : angle 0.79126 / 0.40 (44929) hydrogen bonds : bond 0.05171 / 3.48 ( 1838) hydrogen bonds : angle 5.91928 / 4.13 ( 5427) Misc. bond : bond 0.00584 / 0.39 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 732 time to evaluate : 1.114 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: A 217 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 242 MET cc_start: 0.7799 (mmp) cc_final: 0.7499 (mmp) REVERT: A 320 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.7829 (ttm110) REVERT: A 346 THR cc_start: 0.9282 (m) cc_final: 0.8996 (p) REVERT: A 561 ARG cc_start: 0.8432 (ptt180) cc_final: 0.8003 (mmt180) REVERT: A 631 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7134 (ttm-80) REVERT: A 673 VAL cc_start: 0.8770 (t) cc_final: 0.8289 (p) REVERT: A 776 GLN cc_start: 0.8820 (mt0) cc_final: 0.8571 (tp40) REVERT: B 201 ASN cc_start: 0.7219 (m-40) cc_final: 0.6944 (m-40) REVERT: B 318 GLU cc_start: 0.6365 (mp0) cc_final: 0.6089 (mp0) REVERT: B 320 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7695 (ttm170) REVERT: B 361 HIS cc_start: 0.7214 (m-70) cc_final: 0.6966 (m-70) REVERT: B 430 MET cc_start: 0.3564 (mmm) cc_final: 0.2005 (tmm) REVERT: B 531 VAL cc_start: 0.7886 (t) cc_final: 0.7601 (t) REVERT: B 615 CYS cc_start: 0.7876 (m) cc_final: 0.7614 (t) REVERT: B 782 LEU cc_start: 0.9346 (tp) cc_final: 0.9049 (tt) REVERT: B 846 LEU cc_start: 0.9259 (mt) cc_final: 0.8996 (tt) REVERT: C 232 LEU cc_start: 0.9006 (mt) cc_final: 0.8772 (mt) REVERT: C 257 GLU cc_start: 0.8126 (tt0) cc_final: 0.7722 (tm-30) REVERT: C 260 LYS cc_start: 0.8462 (tttt) cc_final: 0.8088 (mmtt) REVERT: C 498 MET cc_start: 0.5133 (mmm) cc_final: 0.4624 (mmm) REVERT: C 524 MET cc_start: 0.1858 (ttp) cc_final: 0.1591 (ttt) REVERT: C 644 SER cc_start: 0.8478 (m) cc_final: 0.8100 (t) REVERT: C 827 ASN cc_start: 0.8964 (m-40) cc_final: 0.8575 (m-40) REVERT: D 358 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7681 (mm-30) REVERT: D 524 MET cc_start: 0.5150 (mmm) cc_final: 0.4435 (mmt) REVERT: D 691 LEU cc_start: 0.7783 (mt) cc_final: 0.6323 (mt) REVERT: D 774 ILE cc_start: 0.8916 (mt) cc_final: 0.8491 (tp) REVERT: E 495 LEU cc_start: 0.6621 (tt) cc_final: 0.6313 (mm) REVERT: E 540 LEU cc_start: 0.8320 (tp) cc_final: 0.8104 (tt) REVERT: E 562 MET cc_start: 0.8577 (tpt) cc_final: 0.8319 (tpp) REVERT: E 621 PHE cc_start: 0.8265 (t80) cc_final: 0.7677 (t80) REVERT: E 701 ASP cc_start: 0.8362 (p0) cc_final: 0.7792 (t70) REVERT: E 817 LEU cc_start: 0.8890 (tp) cc_final: 0.8689 (tp) REVERT: F 462 TRP cc_start: 0.7844 (t60) cc_final: 0.6424 (t60) REVERT: F 512 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6384 (pt0) REVERT: F 564 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8038 (tp-100) REVERT: F 614 LEU cc_start: 0.8381 (tp) cc_final: 0.7910 (mt) REVERT: F 777 ILE cc_start: 0.8422 (mt) cc_final: 0.7991 (mt) REVERT: F 801 LYS cc_start: 0.9429 (mtpp) cc_final: 0.9065 (mtpt) outliers start: 5 outliers final: 2 residues processed: 736 average time/residue: 0.2141 time to fit residues: 251.8224 Evaluate side-chains 479 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 477 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 284 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 334 GLN A 512 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS A 806 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 361 HIS C 378 HIS C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 GLN D 512 GLN ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 195 GLN F 488 GLN F 567 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.131252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103985 restraints weight = 111248.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106327 restraints weight = 67122.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107695 restraints weight = 47602.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108982 restraints weight = 37990.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.109565 restraints weight = 32713.944| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33304 Z= 0.181 Angle : 0.739 24.264 44929 Z= 0.369 Chirality : 0.045 0.259 5088 Planarity : 0.006 0.065 5869 Dihedral : 7.978 128.082 4638 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4077 helix: 0.04 (0.10), residues: 2390 sheet: -2.53 (0.24), residues: 371 loop : -2.00 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 331 TYR 0.019 0.001 TYR E 671 PHE 0.025 0.002 PHE F 709 TRP 0.014 0.002 TRP D 462 HIS 0.013 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (33285) covalent geometry : angle 0.73855 / 0.37 (44929) hydrogen bonds : bond 0.04633 / 3.11 ( 1838) hydrogen bonds : angle 5.47222 / 3.81 ( 5427) Misc. bond : bond 0.00498 / 0.31 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 636 time to evaluate : 1.224 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: A 242 MET cc_start: 0.7959 (mmp) cc_final: 0.7648 (mmm) REVERT: A 293 MET cc_start: 0.4187 (tpp) cc_final: 0.3383 (mmm) REVERT: A 320 ARG cc_start: 0.8438 (ptp-170) cc_final: 0.8196 (ttm110) REVERT: A 498 MET cc_start: 0.1147 (mmm) cc_final: 0.0795 (mtt) REVERT: A 508 GLU cc_start: 0.3139 (pt0) cc_final: 0.2900 (mt-10) REVERT: A 525 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6886 (tpt170) REVERT: A 561 ARG cc_start: 0.8286 (ptt180) cc_final: 0.7987 (mmt180) REVERT: A 588 ARG cc_start: 0.7300 (mmt90) cc_final: 0.7055 (tmt170) REVERT: A 631 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7295 (ttm-80) REVERT: A 673 VAL cc_start: 0.9006 (t) cc_final: 0.8081 (p) REVERT: B 300 LYS cc_start: 0.8770 (tttt) cc_final: 0.8455 (ttpp) REVERT: B 332 ARG cc_start: 0.8388 (mmt-90) cc_final: 0.7204 (mmt-90) REVERT: B 349 ILE cc_start: 0.8891 (mm) cc_final: 0.8596 (mm) REVERT: B 361 HIS cc_start: 0.7707 (m-70) cc_final: 0.7230 (m-70) REVERT: B 430 MET cc_start: 0.3315 (mmm) cc_final: 0.1937 (tmm) REVERT: B 615 CYS cc_start: 0.7978 (m) cc_final: 0.7682 (t) REVERT: B 622 MET cc_start: 0.7518 (tpp) cc_final: 0.7282 (tpp) REVERT: B 782 LEU cc_start: 0.9320 (tp) cc_final: 0.9108 (tt) REVERT: B 846 LEU cc_start: 0.9370 (mt) cc_final: 0.9029 (tt) REVERT: C 232 LEU cc_start: 0.9130 (mt) cc_final: 0.8803 (mt) REVERT: C 257 GLU cc_start: 0.8387 (tt0) cc_final: 0.7836 (tm-30) REVERT: C 260 LYS cc_start: 0.8401 (tttt) cc_final: 0.8029 (mmtt) REVERT: C 280 LEU cc_start: 0.8860 (tp) cc_final: 0.8612 (tp) REVERT: C 283 MET cc_start: 0.8273 (mtm) cc_final: 0.7835 (mtm) REVERT: C 498 MET cc_start: 0.5059 (mmm) cc_final: 0.4577 (mmm) REVERT: C 615 CYS cc_start: 0.8921 (m) cc_final: 0.8426 (t) REVERT: C 827 ASN cc_start: 0.9129 (m-40) cc_final: 0.8784 (m-40) REVERT: D 204 LEU cc_start: 0.8888 (mm) cc_final: 0.8635 (mm) REVERT: D 396 GLU cc_start: 0.8261 (tp30) cc_final: 0.7974 (tp30) REVERT: D 524 MET cc_start: 0.5239 (mmm) cc_final: 0.4457 (mmt) REVERT: D 723 ASP cc_start: 0.7769 (p0) cc_final: 0.7548 (p0) REVERT: D 725 ILE cc_start: 0.9089 (mt) cc_final: 0.8822 (mt) REVERT: D 774 ILE cc_start: 0.9116 (mt) cc_final: 0.8811 (tt) REVERT: E 283 MET cc_start: 0.8395 (tmm) cc_final: 0.8098 (tmm) REVERT: E 517 THR cc_start: 0.7623 (m) cc_final: 0.7261 (p) REVERT: E 552 MET cc_start: 0.7461 (pmm) cc_final: 0.7212 (pmm) REVERT: E 638 MET cc_start: 0.8058 (pmm) cc_final: 0.7194 (ptm) REVERT: E 687 PHE cc_start: 0.8082 (m-10) cc_final: 0.7729 (m-80) REVERT: E 817 LEU cc_start: 0.9033 (tp) cc_final: 0.8559 (tp) REVERT: E 821 ILE cc_start: 0.8495 (mm) cc_final: 0.8263 (pt) REVERT: F 512 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6564 (pt0) REVERT: F 564 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8045 (tp-100) REVERT: F 716 MET cc_start: 0.9068 (mpp) cc_final: 0.8671 (mpp) REVERT: F 777 ILE cc_start: 0.8128 (mt) cc_final: 0.7464 (mt) REVERT: F 780 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8493 (mtmm) REVERT: F 801 LYS cc_start: 0.9372 (mtpp) cc_final: 0.8981 (mtpt) outliers start: 2 outliers final: 0 residues processed: 638 average time/residue: 0.1993 time to fit residues: 208.2296 Evaluate side-chains 436 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 310 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 297 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 ASN A 334 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 512 GLN B 719 ASN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN C 832 GLN C 858 HIS D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.130512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102996 restraints weight = 102516.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104733 restraints weight = 65668.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105822 restraints weight = 48334.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106199 restraints weight = 39964.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.107149 restraints weight = 36476.864| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33304 Z= 0.176 Angle : 0.719 21.753 44929 Z= 0.361 Chirality : 0.044 0.187 5088 Planarity : 0.005 0.060 5869 Dihedral : 7.751 128.289 4638 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4077 helix: 0.35 (0.10), residues: 2387 sheet: -2.46 (0.24), residues: 392 loop : -1.83 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 750 TYR 0.018 0.002 TYR A 357 PHE 0.022 0.002 PHE E 621 TRP 0.011 0.002 TRP B 462 HIS 0.005 0.001 HIS D 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (33285) covalent geometry : angle 0.71928 / 0.36 (44929) hydrogen bonds : bond 0.04435 / 2.98 ( 1838) hydrogen bonds : angle 5.33676 / 3.71 ( 5427) Misc. bond : bond 0.00587 / 0.40 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 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: A 293 MET cc_start: 0.4624 (tpp) cc_final: 0.4250 (mmt) REVERT: A 318 GLU cc_start: 0.7659 (mp0) cc_final: 0.7231 (mp0) REVERT: A 508 GLU cc_start: 0.3045 (pt0) cc_final: 0.2792 (mt-10) REVERT: A 525 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.6903 (tpt170) REVERT: A 561 ARG cc_start: 0.8508 (ptt180) cc_final: 0.8074 (mmt180) REVERT: A 631 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7203 (ttm-80) REVERT: A 673 VAL cc_start: 0.8958 (t) cc_final: 0.8163 (p) REVERT: B 219 LEU cc_start: 0.9036 (tp) cc_final: 0.8835 (tp) REVERT: B 332 ARG cc_start: 0.8522 (mmt-90) cc_final: 0.7253 (mmt-90) REVERT: B 361 HIS cc_start: 0.7743 (m-70) cc_final: 0.7278 (m-70) REVERT: B 430 MET cc_start: 0.3057 (mmm) cc_final: 0.1783 (tmm) REVERT: B 615 CYS cc_start: 0.7988 (m) cc_final: 0.7761 (t) REVERT: B 782 LEU cc_start: 0.9426 (tp) cc_final: 0.9189 (tp) REVERT: B 846 LEU cc_start: 0.9360 (mt) cc_final: 0.9042 (tt) REVERT: C 196 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7822 (mtm-85) REVERT: C 257 GLU cc_start: 0.8446 (tt0) cc_final: 0.7889 (tm-30) REVERT: C 283 MET cc_start: 0.8029 (mpp) cc_final: 0.7649 (mtm) REVERT: C 318 GLU cc_start: 0.7940 (mp0) cc_final: 0.7157 (mm-30) REVERT: C 498 MET cc_start: 0.5075 (mmm) cc_final: 0.4537 (mmm) REVERT: C 562 MET cc_start: 0.8782 (ttt) cc_final: 0.8574 (ttt) REVERT: C 602 LEU cc_start: 0.8862 (tp) cc_final: 0.8520 (tt) REVERT: C 615 CYS cc_start: 0.8870 (m) cc_final: 0.8399 (t) REVERT: C 688 ASN cc_start: 0.8470 (m-40) cc_final: 0.7745 (m110) REVERT: C 716 MET cc_start: 0.7176 (mtp) cc_final: 0.6846 (ttm) REVERT: C 793 ILE cc_start: 0.9426 (mt) cc_final: 0.9157 (mt) REVERT: C 827 ASN cc_start: 0.9154 (m-40) cc_final: 0.8737 (m-40) REVERT: D 204 LEU cc_start: 0.8795 (mm) cc_final: 0.8576 (mm) REVERT: D 392 ASP cc_start: 0.8224 (t0) cc_final: 0.8013 (t0) REVERT: D 524 MET cc_start: 0.5243 (mmm) cc_final: 0.4418 (mmt) REVERT: D 679 VAL cc_start: 0.8577 (p) cc_final: 0.8217 (p) REVERT: D 691 LEU cc_start: 0.7884 (mt) cc_final: 0.7497 (mt) REVERT: D 723 ASP cc_start: 0.7825 (p0) cc_final: 0.7543 (p0) REVERT: E 283 MET cc_start: 0.8406 (tmm) cc_final: 0.8187 (tmm) REVERT: E 517 THR cc_start: 0.7730 (m) cc_final: 0.7443 (p) REVERT: E 552 MET cc_start: 0.7405 (pmm) cc_final: 0.6688 (pmm) REVERT: E 562 MET cc_start: 0.8720 (tpp) cc_final: 0.8310 (tpt) REVERT: E 621 PHE cc_start: 0.8341 (t80) cc_final: 0.8059 (t80) REVERT: E 638 MET cc_start: 0.8044 (pmm) cc_final: 0.7385 (ptm) REVERT: E 687 PHE cc_start: 0.8233 (m-10) cc_final: 0.7699 (m-80) REVERT: E 817 LEU cc_start: 0.9205 (tp) cc_final: 0.8932 (tp) REVERT: F 330 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6007 (tp30) REVERT: F 629 MET cc_start: 0.8154 (ppp) cc_final: 0.7747 (ppp) REVERT: F 716 MET cc_start: 0.9132 (mpp) cc_final: 0.8661 (mpp) REVERT: F 801 LYS cc_start: 0.9359 (mtpp) cc_final: 0.8932 (mtpt) outliers start: 1 outliers final: 0 residues processed: 587 average time/residue: 0.1943 time to fit residues: 188.9502 Evaluate side-chains 403 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 6 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 chunk 406 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 174 GLN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS E 794 HIS E 824 GLN F 297 ASN F 378 HIS F 454 GLN F 488 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.123802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095307 restraints weight = 115287.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.097533 restraints weight = 71456.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099061 restraints weight = 51386.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099978 restraints weight = 41285.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.100665 restraints weight = 36020.237| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33304 Z= 0.184 Angle : 0.713 22.189 44929 Z= 0.357 Chirality : 0.044 0.196 5088 Planarity : 0.005 0.059 5869 Dihedral : 7.632 126.547 4638 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4077 helix: 0.47 (0.10), residues: 2398 sheet: -2.24 (0.25), residues: 358 loop : -1.74 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 453 TYR 0.015 0.002 TYR C 653 PHE 0.021 0.002 PHE F 621 TRP 0.012 0.002 TRP B 543 HIS 0.013 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (33285) covalent geometry : angle 0.71321 / 0.36 (44929) hydrogen bonds : bond 0.04299 / 2.88 ( 1838) hydrogen bonds : angle 5.24072 / 3.63 ( 5427) Misc. bond : bond 0.00509 / 0.32 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 561 time to evaluate : 1.256 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: A 293 MET cc_start: 0.4487 (tpp) cc_final: 0.4002 (mmt) REVERT: A 318 GLU cc_start: 0.7861 (mp0) cc_final: 0.7623 (mp0) REVERT: A 525 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7130 (tpt170) REVERT: A 561 ARG cc_start: 0.8356 (ptt180) cc_final: 0.8033 (mmt180) REVERT: A 631 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7410 (ttm-80) REVERT: A 717 THR cc_start: 0.8238 (p) cc_final: 0.7994 (p) REVERT: B 186 GLU cc_start: 0.8451 (mp0) cc_final: 0.7871 (mp0) REVERT: B 361 HIS cc_start: 0.7888 (m-70) cc_final: 0.7393 (m-70) REVERT: B 430 MET cc_start: 0.2813 (mmm) cc_final: 0.1696 (tmm) REVERT: B 606 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: B 615 CYS cc_start: 0.7953 (m) cc_final: 0.7733 (t) REVERT: B 629 MET cc_start: 0.8600 (ppp) cc_final: 0.8295 (ppp) REVERT: B 782 LEU cc_start: 0.9263 (tp) cc_final: 0.9001 (tp) REVERT: B 846 LEU cc_start: 0.9455 (mt) cc_final: 0.9073 (tt) REVERT: C 196 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7734 (mtm-85) REVERT: C 257 GLU cc_start: 0.8426 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 283 MET cc_start: 0.8182 (mpp) cc_final: 0.7926 (mpp) REVERT: C 498 MET cc_start: 0.5253 (mmm) cc_final: 0.4761 (mmm) REVERT: C 524 MET cc_start: 0.1476 (ttt) cc_final: 0.0979 (ttp) REVERT: C 535 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8196 (mp0) REVERT: C 615 CYS cc_start: 0.8817 (m) cc_final: 0.8399 (t) REVERT: C 827 ASN cc_start: 0.9193 (m-40) cc_final: 0.8770 (m-40) REVERT: D 524 MET cc_start: 0.5437 (mmm) cc_final: 0.4480 (mmt) REVERT: D 677 ASP cc_start: 0.6803 (t0) cc_final: 0.6481 (t0) REVERT: D 691 LEU cc_start: 0.7928 (mt) cc_final: 0.7508 (mt) REVERT: E 195 GLN cc_start: 0.8148 (pt0) cc_final: 0.7172 (mm-40) REVERT: E 254 GLU cc_start: 0.7044 (mp0) cc_final: 0.6773 (mp0) REVERT: E 517 THR cc_start: 0.7618 (m) cc_final: 0.7358 (p) REVERT: E 546 ILE cc_start: 0.8825 (mm) cc_final: 0.8612 (mm) REVERT: E 562 MET cc_start: 0.8349 (tpp) cc_final: 0.7990 (tpp) REVERT: E 621 PHE cc_start: 0.8416 (t80) cc_final: 0.7901 (t80) REVERT: E 638 MET cc_start: 0.8172 (pmm) cc_final: 0.7661 (ptm) REVERT: E 687 PHE cc_start: 0.8242 (m-10) cc_final: 0.7801 (m-80) REVERT: E 817 LEU cc_start: 0.9240 (tp) cc_final: 0.8979 (tp) REVERT: F 330 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6132 (tp30) outliers start: 2 outliers final: 0 residues processed: 562 average time/residue: 0.1984 time to fit residues: 185.3808 Evaluate side-chains 390 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 153 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 400 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 567 HIS B 568 HIS B 726 GLN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 297 ASN C 361 HIS ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.120356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096200 restraints weight = 115575.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.097054 restraints weight = 80055.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097480 restraints weight = 54534.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097648 restraints weight = 50971.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.097797 restraints weight = 47730.197| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33304 Z= 0.219 Angle : 0.758 21.955 44929 Z= 0.378 Chirality : 0.045 0.211 5088 Planarity : 0.005 0.060 5869 Dihedral : 7.693 125.852 4638 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4077 helix: 0.52 (0.10), residues: 2389 sheet: -2.04 (0.25), residues: 382 loop : -1.79 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 667 TYR 0.023 0.002 TYR F 656 PHE 0.027 0.002 PHE F 621 TRP 0.012 0.002 TRP E 462 HIS 0.017 0.002 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (33285) covalent geometry : angle 0.75780 / 0.38 (44929) hydrogen bonds : bond 0.04421 / 2.97 ( 1838) hydrogen bonds : angle 5.25640 / 3.64 ( 5427) Misc. bond : bond 0.00706 / 0.36 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 1.287 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 242 MET cc_start: 0.7904 (mmm) cc_final: 0.7523 (mmp) REVERT: A 293 MET cc_start: 0.4548 (tpp) cc_final: 0.4069 (mmt) REVERT: A 525 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7202 (tpt170) REVERT: A 561 ARG cc_start: 0.8356 (ptt180) cc_final: 0.8053 (mmt180) REVERT: A 631 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7259 (ttm-80) REVERT: B 361 HIS cc_start: 0.8082 (m-70) cc_final: 0.6687 (m-70) REVERT: B 430 MET cc_start: 0.2551 (mmm) cc_final: 0.1509 (tmm) REVERT: B 528 ARG cc_start: 0.7818 (mtt180) cc_final: 0.5862 (mmt180) REVERT: B 629 MET cc_start: 0.8517 (ppp) cc_final: 0.8176 (ppp) REVERT: B 782 LEU cc_start: 0.9212 (tp) cc_final: 0.8921 (tp) REVERT: B 846 LEU cc_start: 0.9529 (mt) cc_final: 0.9125 (tt) REVERT: C 196 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7719 (mtm-85) REVERT: C 257 GLU cc_start: 0.8519 (tt0) cc_final: 0.7991 (tm-30) REVERT: C 498 MET cc_start: 0.5360 (mmm) cc_final: 0.4858 (mmm) REVERT: C 595 ASN cc_start: 0.6051 (p0) cc_final: 0.5791 (p0) REVERT: C 615 CYS cc_start: 0.8751 (m) cc_final: 0.8320 (t) REVERT: C 827 ASN cc_start: 0.9063 (m-40) cc_final: 0.8576 (m-40) REVERT: D 317 ASP cc_start: 0.7909 (p0) cc_final: 0.7707 (p0) REVERT: D 524 MET cc_start: 0.5576 (mmm) cc_final: 0.4394 (mmt) REVERT: D 723 ASP cc_start: 0.8029 (p0) cc_final: 0.7734 (p0) REVERT: E 195 GLN cc_start: 0.8305 (pt0) cc_final: 0.7125 (mm-40) REVERT: E 517 THR cc_start: 0.7598 (m) cc_final: 0.7347 (p) REVERT: E 562 MET cc_start: 0.8210 (tpp) cc_final: 0.7668 (tpt) REVERT: E 638 MET cc_start: 0.8304 (pmm) cc_final: 0.7363 (ptt) REVERT: E 708 ASP cc_start: 0.6978 (t0) cc_final: 0.6759 (p0) REVERT: E 817 LEU cc_start: 0.9238 (tp) cc_final: 0.9026 (tp) REVERT: F 330 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6582 (tp30) REVERT: F 498 MET cc_start: 0.6354 (tpp) cc_final: 0.5825 (tpp) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1895 time to fit residues: 167.0621 Evaluate side-chains 375 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 374 optimal weight: 7.9990 chunk 386 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 366 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 HIS ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 201 ASN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 HIS ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS F 711 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.120485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094605 restraints weight = 115945.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096926 restraints weight = 73120.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097626 restraints weight = 49893.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098237 restraints weight = 38820.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098338 restraints weight = 37582.426| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33304 Z= 0.196 Angle : 0.736 21.100 44929 Z= 0.368 Chirality : 0.045 0.218 5088 Planarity : 0.005 0.058 5869 Dihedral : 7.657 124.548 4638 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4077 helix: 0.57 (0.10), residues: 2403 sheet: -2.05 (0.26), residues: 373 loop : -1.70 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 645 TYR 0.036 0.002 TYR F 656 PHE 0.025 0.002 PHE F 621 TRP 0.010 0.002 TRP B 462 HIS 0.014 0.001 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (33285) covalent geometry : angle 0.73639 / 0.37 (44929) hydrogen bonds : bond 0.04358 / 2.94 ( 1838) hydrogen bonds : angle 5.21990 / 3.62 ( 5427) Misc. bond : bond 0.00517 / 0.32 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 527 time to evaluate : 1.196 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 242 MET cc_start: 0.8058 (mmm) cc_final: 0.7548 (mmp) REVERT: A 293 MET cc_start: 0.4448 (tpp) cc_final: 0.3984 (mmt) REVERT: A 318 GLU cc_start: 0.7961 (mp0) cc_final: 0.7592 (mp0) REVERT: A 525 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7209 (tpt170) REVERT: A 561 ARG cc_start: 0.8372 (ptt180) cc_final: 0.8047 (mmt180) REVERT: A 631 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7505 (ttm-80) REVERT: A 852 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8184 (tmt170) REVERT: A 854 VAL cc_start: 0.7190 (p) cc_final: 0.6441 (p) REVERT: B 430 MET cc_start: 0.2600 (mmm) cc_final: 0.1904 (ttm) REVERT: B 528 ARG cc_start: 0.7732 (mtt180) cc_final: 0.5733 (mmt180) REVERT: B 606 PRO cc_start: 0.8727 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: B 629 MET cc_start: 0.8614 (ppp) cc_final: 0.8261 (ppp) REVERT: B 782 LEU cc_start: 0.9245 (tp) cc_final: 0.9001 (tp) REVERT: B 846 LEU cc_start: 0.9529 (mt) cc_final: 0.9170 (tp) REVERT: C 196 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7819 (mtm-85) REVERT: C 257 GLU cc_start: 0.8560 (tt0) cc_final: 0.8053 (tm-30) REVERT: C 498 MET cc_start: 0.5152 (mmm) cc_final: 0.4912 (tpp) REVERT: C 524 MET cc_start: 0.2070 (ttt) cc_final: 0.1550 (ttp) REVERT: C 615 CYS cc_start: 0.8947 (m) cc_final: 0.8473 (t) REVERT: C 737 MET cc_start: 0.7574 (ppp) cc_final: 0.7282 (ppp) REVERT: C 827 ASN cc_start: 0.9135 (m-40) cc_final: 0.8666 (m-40) REVERT: D 191 ILE cc_start: 0.8394 (mm) cc_final: 0.7758 (mm) REVERT: D 524 MET cc_start: 0.5497 (mmm) cc_final: 0.4388 (mmt) REVERT: D 691 LEU cc_start: 0.8185 (mm) cc_final: 0.7834 (mm) REVERT: D 723 ASP cc_start: 0.8290 (p0) cc_final: 0.7969 (p0) REVERT: E 195 GLN cc_start: 0.8291 (pt0) cc_final: 0.7244 (mm-40) REVERT: E 242 MET cc_start: 0.8354 (mmp) cc_final: 0.8149 (mpp) REVERT: E 350 LEU cc_start: 0.9171 (mm) cc_final: 0.8797 (tp) REVERT: E 475 ILE cc_start: 0.8099 (pt) cc_final: 0.7788 (pt) REVERT: E 552 MET cc_start: 0.6943 (pmm) cc_final: 0.6585 (pmm) REVERT: E 562 MET cc_start: 0.8065 (tpp) cc_final: 0.7516 (tpp) REVERT: E 638 MET cc_start: 0.8282 (pmm) cc_final: 0.7318 (ptt) REVERT: E 708 ASP cc_start: 0.7172 (t0) cc_final: 0.6937 (p0) REVERT: F 298 MET cc_start: 0.5709 (mmm) cc_final: 0.5485 (mmt) REVERT: F 330 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6630 (tp30) REVERT: F 401 ILE cc_start: 0.8481 (mm) cc_final: 0.8114 (mm) REVERT: F 629 MET cc_start: 0.8421 (ppp) cc_final: 0.8153 (ppp) REVERT: F 763 PHE cc_start: 0.8078 (m-80) cc_final: 0.7823 (m-80) REVERT: F 777 ILE cc_start: 0.8408 (mt) cc_final: 0.7858 (mt) REVERT: F 780 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8422 (mtmm) outliers start: 1 outliers final: 0 residues processed: 528 average time/residue: 0.1826 time to fit residues: 160.7706 Evaluate side-chains 362 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 268 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 770 HIS B 849 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS F 426 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.130352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.104180 restraints weight = 103631.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105858 restraints weight = 69368.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107209 restraints weight = 52870.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107741 restraints weight = 43220.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108167 restraints weight = 39165.970| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33304 Z= 0.141 Angle : 0.696 20.135 44929 Z= 0.344 Chirality : 0.043 0.199 5088 Planarity : 0.005 0.056 5869 Dihedral : 7.504 123.808 4638 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4077 helix: 0.82 (0.11), residues: 2400 sheet: -1.97 (0.26), residues: 378 loop : -1.60 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 497 TYR 0.027 0.001 TYR F 656 PHE 0.021 0.002 PHE F 621 TRP 0.011 0.001 TRP B 462 HIS 0.009 0.001 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (33285) covalent geometry : angle 0.69606 / 0.34 (44929) hydrogen bonds : bond 0.04109 / 2.77 ( 1838) hydrogen bonds : angle 5.01605 / 3.48 ( 5427) Misc. bond : bond 0.00486 / 0.30 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.215 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: A 293 MET cc_start: 0.4670 (tpp) cc_final: 0.4283 (mmt) REVERT: A 318 GLU cc_start: 0.7387 (mp0) cc_final: 0.7028 (mp0) REVERT: A 525 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7098 (tpt170) REVERT: A 561 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8065 (mmt180) REVERT: A 631 ARG cc_start: 0.7692 (ttt180) cc_final: 0.7323 (ttm-80) REVERT: A 854 VAL cc_start: 0.7311 (p) cc_final: 0.6283 (p) REVERT: B 430 MET cc_start: 0.2550 (mmm) cc_final: 0.1850 (ttm) REVERT: B 528 ARG cc_start: 0.7649 (mtt180) cc_final: 0.5658 (mmt180) REVERT: B 606 PRO cc_start: 0.8529 (Cg_exo) cc_final: 0.8029 (Cg_endo) REVERT: B 629 MET cc_start: 0.8379 (ppp) cc_final: 0.8079 (ppp) REVERT: B 737 MET cc_start: 0.5653 (mmt) cc_final: 0.5218 (mmt) REVERT: B 846 LEU cc_start: 0.9370 (mt) cc_final: 0.9072 (tt) REVERT: C 196 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7651 (mtm-85) REVERT: C 257 GLU cc_start: 0.8382 (tt0) cc_final: 0.7915 (tm-30) REVERT: C 615 CYS cc_start: 0.8725 (m) cc_final: 0.8245 (t) REVERT: C 737 MET cc_start: 0.7013 (ppp) cc_final: 0.6707 (ppp) REVERT: C 827 ASN cc_start: 0.9011 (m-40) cc_final: 0.8506 (m-40) REVERT: D 524 MET cc_start: 0.5360 (mmm) cc_final: 0.4197 (mmt) REVERT: E 195 GLN cc_start: 0.8064 (pt0) cc_final: 0.7158 (mm-40) REVERT: E 350 LEU cc_start: 0.9057 (mm) cc_final: 0.8625 (tp) REVERT: E 370 ILE cc_start: 0.8935 (mt) cc_final: 0.8724 (mt) REVERT: E 475 ILE cc_start: 0.8454 (pt) cc_final: 0.8116 (pt) REVERT: E 552 MET cc_start: 0.7328 (pmm) cc_final: 0.6762 (pmm) REVERT: E 562 MET cc_start: 0.7949 (tpp) cc_final: 0.7377 (tpp) REVERT: E 564 GLN cc_start: 0.7570 (tt0) cc_final: 0.7271 (mp10) REVERT: E 638 MET cc_start: 0.8154 (pmm) cc_final: 0.7105 (ptt) REVERT: E 687 PHE cc_start: 0.8287 (m-10) cc_final: 0.7789 (m-80) REVERT: F 167 ASP cc_start: 0.7187 (t0) cc_final: 0.6416 (t0) REVERT: F 240 LEU cc_start: 0.6759 (tp) cc_final: 0.6317 (tt) REVERT: F 330 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6652 (tp30) REVERT: F 401 ILE cc_start: 0.8450 (mm) cc_final: 0.8079 (mm) REVERT: F 405 ILE cc_start: 0.6304 (mm) cc_final: 0.6104 (mm) REVERT: F 629 MET cc_start: 0.8547 (ppp) cc_final: 0.8243 (ppp) REVERT: F 684 PRO cc_start: 0.6532 (Cg_exo) cc_final: 0.6284 (Cg_endo) REVERT: F 777 ILE cc_start: 0.8186 (mt) cc_final: 0.7688 (mt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1899 time to fit residues: 172.5372 Evaluate side-chains 387 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 246 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 321 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 726 GLN B 770 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS F 174 GLN F 195 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.121547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098231 restraints weight = 112299.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099149 restraints weight = 77792.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099246 restraints weight = 56121.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099650 restraints weight = 51316.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099817 restraints weight = 45535.596| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33304 Z= 0.178 Angle : 0.734 19.963 44929 Z= 0.364 Chirality : 0.045 0.231 5088 Planarity : 0.005 0.067 5869 Dihedral : 7.549 121.547 4638 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.03 % Allowed : 0.64 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4077 helix: 0.80 (0.10), residues: 2399 sheet: -1.86 (0.26), residues: 383 loop : -1.65 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 756 TYR 0.022 0.002 TYR F 656 PHE 0.021 0.002 PHE F 621 TRP 0.008 0.001 TRP E 462 HIS 0.011 0.001 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (33285) covalent geometry : angle 0.73352 / 0.36 (44929) hydrogen bonds : bond 0.04205 / 2.83 ( 1838) hydrogen bonds : angle 5.06672 / 3.51 ( 5427) Misc. bond : bond 0.00505 / 0.31 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4760 (tpp) cc_final: 0.4220 (mmt) REVERT: A 315 THR cc_start: 0.8483 (m) cc_final: 0.8243 (m) REVERT: A 318 GLU cc_start: 0.7819 (mp0) cc_final: 0.7368 (mp0) REVERT: A 358 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6803 (mt-10) REVERT: A 525 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7261 (ttt180) REVERT: A 561 ARG cc_start: 0.8281 (ptt180) cc_final: 0.8057 (mmt180) REVERT: A 631 ARG cc_start: 0.7965 (ttt180) cc_final: 0.7533 (ttm-80) REVERT: B 430 MET cc_start: 0.2579 (mmm) cc_final: 0.1892 (ttm) REVERT: B 528 ARG cc_start: 0.7883 (mtt180) cc_final: 0.5986 (mmt180) REVERT: B 606 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8251 (Cg_endo) REVERT: B 629 MET cc_start: 0.8587 (ppp) cc_final: 0.8122 (ppp) REVERT: B 846 LEU cc_start: 0.9456 (mt) cc_final: 0.9078 (tt) REVERT: C 257 GLU cc_start: 0.8440 (tt0) cc_final: 0.7896 (tm-30) REVERT: C 498 MET cc_start: 0.4353 (tpt) cc_final: 0.3690 (tpt) REVERT: C 615 CYS cc_start: 0.8529 (m) cc_final: 0.8217 (t) REVERT: C 677 ASP cc_start: 0.6424 (t70) cc_final: 0.6165 (t70) REVERT: C 737 MET cc_start: 0.7379 (ppp) cc_final: 0.7119 (ppp) REVERT: C 827 ASN cc_start: 0.8962 (m-40) cc_final: 0.8460 (m-40) REVERT: D 524 MET cc_start: 0.5296 (mmm) cc_final: 0.4190 (mmt) REVERT: E 195 GLN cc_start: 0.8303 (pt0) cc_final: 0.7228 (mm-40) REVERT: E 350 LEU cc_start: 0.9086 (mm) cc_final: 0.8635 (tp) REVERT: E 370 ILE cc_start: 0.8892 (mt) cc_final: 0.8626 (mt) REVERT: E 443 MET cc_start: 0.6138 (tmm) cc_final: 0.3592 (mtt) REVERT: E 475 ILE cc_start: 0.8221 (pt) cc_final: 0.7874 (pt) REVERT: E 552 MET cc_start: 0.7415 (pmm) cc_final: 0.6814 (pmm) REVERT: E 562 MET cc_start: 0.7912 (tpp) cc_final: 0.7585 (tpp) REVERT: E 564 GLN cc_start: 0.7612 (tt0) cc_final: 0.7333 (mp10) REVERT: E 638 MET cc_start: 0.8203 (pmm) cc_final: 0.7152 (ptt) REVERT: E 687 PHE cc_start: 0.8236 (m-10) cc_final: 0.7922 (m-80) REVERT: E 762 VAL cc_start: 0.8909 (t) cc_final: 0.8593 (p) REVERT: F 245 LEU cc_start: 0.5122 (mm) cc_final: 0.4904 (mm) REVERT: F 330 GLU cc_start: 0.7953 (tm-30) cc_final: 0.6698 (tp30) REVERT: F 401 ILE cc_start: 0.8558 (mm) cc_final: 0.8212 (mm) REVERT: F 407 SER cc_start: 0.6003 (p) cc_final: 0.5482 (p) REVERT: F 462 TRP cc_start: 0.7834 (t60) cc_final: 0.6009 (t60) REVERT: F 498 MET cc_start: 0.6468 (tpp) cc_final: 0.5968 (tpp) REVERT: F 629 MET cc_start: 0.8527 (ppp) cc_final: 0.8231 (ppp) REVERT: F 684 PRO cc_start: 0.6557 (Cg_exo) cc_final: 0.6301 (Cg_endo) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.1869 time to fit residues: 158.9948 Evaluate side-chains 369 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 267 optimal weight: 7.9990 chunk 238 optimal weight: 0.4980 chunk 274 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.121720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.098558 restraints weight = 113226.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099335 restraints weight = 78093.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099704 restraints weight = 55961.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100106 restraints weight = 50586.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.100165 restraints weight = 45528.482| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33304 Z= 0.166 Angle : 0.725 19.829 44929 Z= 0.360 Chirality : 0.044 0.208 5088 Planarity : 0.005 0.056 5869 Dihedral : 7.542 121.019 4638 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4077 helix: 0.83 (0.11), residues: 2414 sheet: -1.76 (0.25), residues: 391 loop : -1.64 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 491 TYR 0.020 0.002 TYR F 656 PHE 0.024 0.002 PHE B 333 TRP 0.009 0.001 TRP B 462 HIS 0.009 0.001 HIS D 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (33285) covalent geometry : angle 0.72538 / 0.36 (44929) hydrogen bonds : bond 0.04106 / 2.77 ( 1838) hydrogen bonds : angle 5.06217 / 3.51 ( 5427) Misc. bond : bond 0.00493 / 0.31 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 513 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4726 (tpp) cc_final: 0.4239 (mmt) REVERT: A 315 THR cc_start: 0.8455 (m) cc_final: 0.8225 (m) REVERT: A 318 GLU cc_start: 0.7847 (mp0) cc_final: 0.7376 (mp0) REVERT: A 525 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7438 (ttm170) REVERT: A 631 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7389 (ttm-80) REVERT: B 430 MET cc_start: 0.2720 (mmm) cc_final: 0.2052 (ttm) REVERT: B 528 ARG cc_start: 0.7950 (mtt180) cc_final: 0.5967 (mmt180) REVERT: B 606 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8296 (Cg_endo) REVERT: B 629 MET cc_start: 0.8585 (ppp) cc_final: 0.8130 (ppp) REVERT: B 633 ASP cc_start: 0.7448 (p0) cc_final: 0.6922 (p0) REVERT: B 737 MET cc_start: 0.5880 (mmt) cc_final: 0.5501 (mmt) REVERT: B 846 LEU cc_start: 0.9444 (mt) cc_final: 0.9062 (tt) REVERT: C 257 GLU cc_start: 0.8457 (tt0) cc_final: 0.7778 (tm-30) REVERT: C 403 MET cc_start: 0.9008 (tpp) cc_final: 0.8771 (tpp) REVERT: C 498 MET cc_start: 0.4320 (tpt) cc_final: 0.3701 (tpt) REVERT: C 615 CYS cc_start: 0.8562 (m) cc_final: 0.8229 (t) REVERT: C 737 MET cc_start: 0.7397 (ppp) cc_final: 0.7133 (ppp) REVERT: C 827 ASN cc_start: 0.8973 (m-40) cc_final: 0.8470 (m-40) REVERT: D 232 LEU cc_start: 0.8185 (mt) cc_final: 0.7969 (mt) REVERT: D 524 MET cc_start: 0.5292 (mmm) cc_final: 0.4079 (mmt) REVERT: E 195 GLN cc_start: 0.8249 (pt0) cc_final: 0.7235 (mm-40) REVERT: E 242 MET cc_start: 0.8776 (mmm) cc_final: 0.8228 (mpp) REVERT: E 443 MET cc_start: 0.6029 (tmm) cc_final: 0.3503 (mtt) REVERT: E 475 ILE cc_start: 0.8257 (pt) cc_final: 0.7878 (pt) REVERT: E 552 MET cc_start: 0.7546 (pmm) cc_final: 0.6864 (pmm) REVERT: E 562 MET cc_start: 0.7897 (tpp) cc_final: 0.7616 (tpp) REVERT: E 564 GLN cc_start: 0.7622 (tt0) cc_final: 0.7351 (mp10) REVERT: E 638 MET cc_start: 0.8233 (pmm) cc_final: 0.7448 (ptp) REVERT: E 687 PHE cc_start: 0.8318 (m-10) cc_final: 0.7842 (m-80) REVERT: E 762 VAL cc_start: 0.8898 (t) cc_final: 0.8602 (p) REVERT: F 330 GLU cc_start: 0.8043 (tm-30) cc_final: 0.6818 (tp30) REVERT: F 401 ILE cc_start: 0.8489 (mm) cc_final: 0.7425 (mm) REVERT: F 405 ILE cc_start: 0.6191 (mm) cc_final: 0.5874 (mm) REVERT: F 462 TRP cc_start: 0.7816 (t60) cc_final: 0.6021 (t60) REVERT: F 498 MET cc_start: 0.6396 (tpp) cc_final: 0.5903 (tpp) REVERT: F 629 MET cc_start: 0.8506 (ppp) cc_final: 0.8216 (ppp) REVERT: F 684 PRO cc_start: 0.6723 (Cg_exo) cc_final: 0.6471 (Cg_endo) outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.1850 time to fit residues: 159.3274 Evaluate side-chains 370 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 239 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 806 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.119470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096349 restraints weight = 113750.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.097539 restraints weight = 76512.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.097939 restraints weight = 53424.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098339 restraints weight = 47709.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098353 restraints weight = 44310.892| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33304 Z= 0.230 Angle : 0.799 20.398 44929 Z= 0.398 Chirality : 0.046 0.204 5088 Planarity : 0.005 0.072 5869 Dihedral : 7.720 120.249 4638 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4077 helix: 0.57 (0.10), residues: 2420 sheet: -1.86 (0.26), residues: 385 loop : -1.69 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 497 TYR 0.020 0.002 TYR D 656 PHE 0.033 0.002 PHE F 621 TRP 0.010 0.002 TRP E 462 HIS 0.011 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (33285) covalent geometry : angle 0.79919 / 0.40 (44929) hydrogen bonds : bond 0.04474 / 3.02 ( 1838) hydrogen bonds : angle 5.26158 / 3.64 ( 5427) Misc. bond : bond 0.00510 / 0.32 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.29 seconds wall clock time: 101 minutes 18.22 seconds (6078.22 seconds total)