Starting phenix.real_space_refine on Fri Mar 6 07:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.map" model { file = "/net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs6_4624/03_2026/6qs6_4624.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 109 5.16 5 C 17822 2.51 5 N 5179 2.21 5 O 5416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28557 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} 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: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} 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: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} 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: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.24 Number of scatterers: 28557 At special positions: 0 Unit cell: (123.9, 145.95, 150.15, 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 109 16.00 P 31 15.00 O 5416 8.00 N 5179 7.00 C 17822 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 30 sheets defined 59.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.735A pdb=" N LEU A 245 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 246' Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.990A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.816A pdb=" N PHE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 366 through 380 Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.789A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.521A pdb=" N LYS A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.556A pdb=" N VAL A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.526A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 653 through 659 removed outlier: 4.574A pdb=" N GLU A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 658 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 659 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.833A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 removed outlier: 3.595A pdb=" N PHE A 729 " --> pdb=" O ILE A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 750 through 756 removed outlier: 3.596A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 807 removed outlier: 3.536A pdb=" N LEU A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.687A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.974A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.703A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Proline residue: B 301 - end of helix removed outlier: 4.033A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.870A pdb=" N PHE B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.598A pdb=" N THR B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.710A pdb=" N ILE B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 408 removed outlier: 4.295A pdb=" N LYS B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 552 through 570 Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.525A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 623 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 639 through 642 removed outlier: 3.619A pdb=" N SER B 642 " --> pdb=" O GLU B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 660 through 669 Processing helix chain 'B' and resid 679 through 682 removed outlier: 3.943A pdb=" N ALA B 682 " --> pdb=" O VAL B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 683 through 686 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 733 through 749 Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 814 through 835 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 253 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.374A pdb=" N ALA C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 326 through 332 Processing helix chain 'C' and resid 342 through 362 Processing helix chain 'C' and resid 366 through 381 removed outlier: 3.713A pdb=" N ILE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.709A pdb=" N SER C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 444 through 465 Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 552 through 561 removed outlier: 3.682A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 573 through 589 removed outlier: 3.680A 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 639 through 642 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 660 through 669 Processing helix chain 'C' and resid 679 through 682 removed outlier: 3.757A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.965A pdb=" N PHE C 687 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 removed outlier: 3.507A pdb=" N MET C 737 " --> pdb=" O ASP C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.697A pdb=" N ILE C 757 " --> pdb=" O PHE C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 790 removed outlier: 3.819A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 807 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 211 through 226 Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.565A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.659A pdb=" N MET D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 285' Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.563A pdb=" N ILE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 362 Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 427 Processing helix chain 'D' and resid 444 through 465 Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.698A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.538A pdb=" N ARG D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 568 Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.649A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 589 " --> pdb=" O ARG D 585 " (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 641 through 646 removed outlier: 3.919A pdb=" N SER D 644 " --> pdb=" O HIS D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.863A pdb=" N GLU D 658 " --> pdb=" O GLY D 655 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.514A pdb=" N ALA D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.532A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 697 removed outlier: 4.127A pdb=" N PHE D 687 " --> pdb=" O HIS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 Processing helix chain 'D' and resid 750 through 756 removed outlier: 3.572A pdb=" N ILE D 754 " --> pdb=" O ARG D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 807 Processing helix chain 'D' and resid 814 through 825 removed outlier: 3.695A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 835 Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 242 through 248 removed outlier: 3.828A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 270 removed outlier: 3.634A pdb=" N GLU E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.540A pdb=" N GLY E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 304 removed outlier: 3.737A pdb=" N ALA E 302 " --> pdb=" O MET E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 342 through 362 removed outlier: 3.564A pdb=" N THR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 532 through 542 removed outlier: 3.584A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 561 removed outlier: 3.729A pdb=" N ARG E 561 " --> pdb=" O GLU E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 570 Processing helix chain 'E' and resid 573 through 590 removed outlier: 3.654A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 624 removed outlier: 3.656A pdb=" N LEU E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 637 No H-bonds generated for 'chain 'E' and resid 635 through 637' Processing helix chain 'E' and resid 640 through 648 Processing helix chain 'E' and resid 663 through 668 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.546A pdb=" N LYS E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 697 removed outlier: 3.866A pdb=" N PHE E 687 " --> pdb=" O HIS E 683 " (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 756 Processing helix chain 'E' and resid 767 through 790 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 814 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 211 through 226 Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.582A 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 285 Processing helix chain 'F' and resid 299 through 306 removed outlier: 3.679A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.798A pdb=" N ARG F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 406 removed outlier: 3.642A pdb=" N ASP F 406 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 555 through 570 removed outlier: 3.529A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 590 removed outlier: 4.319A pdb=" N VAL F 577 " --> pdb=" O GLN F 573 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY F 590 " --> pdb=" O ARG F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 623 removed outlier: 3.576A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 646 Processing helix chain 'F' and resid 653 through 657 removed outlier: 3.964A pdb=" N TYR F 656 " --> pdb=" O TYR F 653 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU F 657 " --> pdb=" O VAL F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 653 through 657' Processing helix chain 'F' and resid 663 through 669 removed outlier: 3.558A pdb=" N ARG F 668 " --> pdb=" O GLU F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.672A pdb=" N ALA F 682 " --> pdb=" O VAL F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 697 removed outlier: 3.536A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 727 removed outlier: 3.537A pdb=" N ILE F 725 " --> pdb=" O GLY F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 749 Processing helix chain 'F' and resid 750 through 757 removed outlier: 3.590A pdb=" N ILE F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.655A pdb=" N ILE F 771 " --> pdb=" O GLY F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 813 through 834 removed outlier: 3.595A pdb=" N LEU F 817 " --> pdb=" O GLY F 813 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.558A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (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 364 through 365 removed outlier: 7.149A pdb=" N GLN A 364 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 633 removed outlier: 6.422A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 600 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 761 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU A 602 " --> pdb=" O VAL A 761 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.561A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 792 through 795 removed outlier: 6.903A pdb=" N GLU A 792 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU A 846 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N HIS A 794 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL A 848 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.538A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL B 311 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 275 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 203 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.269A 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 633 removed outlier: 6.795A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 716 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER B 600 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL B 761 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU B 602 " --> pdb=" O VAL B 761 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 698 through 701 removed outlier: 3.868A pdb=" N ARG B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AB3, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.850A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.894A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 631 removed outlier: 6.387A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY C 599 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET C 716 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 602 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB7, first strand: chain 'C' and resid 792 through 795 removed outlier: 6.883A pdb=" N GLU C 792 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU C 846 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N HIS C 794 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.509A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL D 311 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D 275 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA D 313 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE D 277 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN D 201 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 336 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL D 203 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 364 through 365 removed outlier: 7.236A pdb=" N GLN D 364 " --> pdb=" O VAL D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 630 through 633 removed outlier: 3.548A pdb=" N THR D 717 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER D 600 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 761 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU D 602 " --> pdb=" O VAL D 761 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.528A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 236 through 238 removed outlier: 6.247A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 599 through 603 removed outlier: 6.100A pdb=" N ILE E 674 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR E 717 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU E 676 " --> pdb=" O THR E 717 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 698 through 700 Processing sheet with id=AC6, first strand: chain 'E' and resid 792 through 795 removed outlier: 6.554A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 845 " --> pdb=" O VAL E 856 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.497A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 312 through 315 removed outlier: 7.834A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.509A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 599 through 603 removed outlier: 5.546A pdb=" N GLY F 599 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET F 716 " --> pdb=" O GLY F 599 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE F 601 " --> pdb=" O MET F 716 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 698 through 700 removed outlier: 3.501A pdb=" N VAL F 707 " --> pdb=" O LEU F 699 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 793 through 795 1422 hydrogen bonds defined for protein. 4203 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: 5.66 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10116 1.36 - 1.50: 8035 1.50 - 1.65: 10640 1.65 - 1.80: 152 1.80 - 1.94: 45 Bond restraints: 28988 Sorted by residual: bond pdb=" CB GLN C 692 " pdb=" CG GLN C 692 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CB VAL D 580 " pdb=" CG1 VAL D 580 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG GLN C 692 " pdb=" CD GLN C 692 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.23e+00 bond pdb=" CB LEU D 618 " pdb=" CG LEU D 618 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" CB GLN B 692 " pdb=" CG GLN B 692 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.37e+00 ... (remaining 28983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 37917 2.71 - 5.41: 1093 5.41 - 8.12: 144 8.12 - 10.82: 26 10.82 - 13.53: 5 Bond angle restraints: 39185 Sorted by residual: angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 112.96 106.52 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" N VAL E 666 " pdb=" CA VAL E 666 " pdb=" C VAL E 666 " ideal model delta sigma weight residual 112.96 107.50 5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" C LEU B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 127.00 136.59 -9.59 2.40e+00 1.74e-01 1.60e+01 angle pdb=" N ARG D 815 " pdb=" CA ARG D 815 " pdb=" C ARG D 815 " ideal model delta sigma weight residual 109.81 118.48 -8.67 2.21e+00 2.05e-01 1.54e+01 ... (remaining 39180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 17596 32.10 - 64.19: 242 64.19 - 96.29: 19 96.29 - 128.39: 2 128.39 - 160.48: 2 Dihedral angle restraints: 17861 sinusoidal: 7544 harmonic: 10317 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 142.77 37.23 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" O1B ADP A1002 " pdb=" O3A ADP A1002 " pdb=" PB ADP A1002 " pdb=" PA ADP A1002 " ideal model delta sinusoidal sigma weight residual 300.00 139.51 160.48 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 72.63 -132.62 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 17858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3330 0.067 - 0.134: 962 0.134 - 0.200: 133 0.200 - 0.267: 8 0.267 - 0.334: 3 Chirality restraints: 4436 Sorted by residual: chirality pdb=" CB ILE B 205 " pdb=" CA ILE B 205 " pdb=" CG1 ILE B 205 " pdb=" CG2 ILE B 205 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.20e+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 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4433 not shown) Planarity restraints: 5114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO D 684 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE C 763 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.014 2.00e-02 2.50e+03 1.87e-02 9.58e+00 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.051 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " 0.002 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.013 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.016 2.00e-02 2.50e+03 ... (remaining 5111 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2504 2.73 - 3.27: 27522 3.27 - 3.81: 46896 3.81 - 4.36: 56251 4.36 - 4.90: 96420 Nonbonded interactions: 229593 Sorted by model distance: nonbonded pdb=" O2A AGS D 902 " pdb=" O2B AGS D 902 " model vdw 2.187 3.040 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.226 3.040 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.231 3.040 nonbonded pdb=" O2A AGS C1002 " pdb=" O2B AGS C1002 " model vdw 2.236 3.040 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.238 3.040 ... (remaining 229588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 858)) selection = (chain 'E' and resid 159 through 858) selection = (chain 'F' and resid 159 through 858) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.860 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.104 29005 Z= 0.443 Angle : 1.090 13.526 39185 Z= 0.578 Chirality : 0.061 0.334 4436 Planarity : 0.008 0.089 5114 Dihedral : 11.075 160.483 11209 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.11), residues: 3532 helix: -2.38 (0.09), residues: 1931 sheet: -3.20 (0.24), residues: 372 loop : -2.74 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 815 TYR 0.026 0.003 TYR C 357 PHE 0.050 0.005 PHE C 763 TRP 0.035 0.005 TRP B 543 HIS 0.015 0.002 HIS C 567 Details of bonding type rmsd covalent geometry : bond 0.01070 (28988) covalent geometry : angle 1.09030 (39185) hydrogen bonds : bond 0.16865 ( 1422) hydrogen bonds : angle 7.91422 ( 4203) Misc. bond : bond 0.00510 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1026 time to evaluate : 0.870 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: A 169 THR cc_start: 0.5676 (p) cc_final: 0.4342 (p) REVERT: A 391 ILE cc_start: 0.5904 (mt) cc_final: 0.5670 (tp) REVERT: A 394 ILE cc_start: 0.5916 (mm) cc_final: 0.4805 (mt) REVERT: B 783 TYR cc_start: 0.6315 (m-10) cc_final: 0.6086 (m-10) REVERT: B 821 ILE cc_start: 0.7067 (mt) cc_final: 0.6706 (mt) REVERT: C 800 LEU cc_start: 0.8488 (tt) cc_final: 0.7634 (mp) REVERT: D 459 GLU cc_start: 0.5364 (tt0) cc_final: 0.5048 (tp30) REVERT: D 578 ASP cc_start: 0.2147 (m-30) cc_final: 0.1885 (m-30) REVERT: D 598 ILE cc_start: 0.7148 (mt) cc_final: 0.6860 (tp) REVERT: D 808 TYR cc_start: 0.3433 (t80) cc_final: 0.3052 (t80) REVERT: E 406 ASP cc_start: 0.3797 (t0) cc_final: 0.3360 (t70) REVERT: E 744 VAL cc_start: 0.6902 (t) cc_final: 0.6598 (t) REVERT: F 297 ASN cc_start: 0.7041 (m110) cc_final: 0.6723 (m-40) REVERT: F 392 ASP cc_start: 0.5669 (m-30) cc_final: 0.4943 (m-30) REVERT: F 707 VAL cc_start: 0.1847 (t) cc_final: 0.1628 (t) REVERT: F 795 ILE cc_start: 0.6473 (tt) cc_final: 0.6257 (tt) outliers start: 2 outliers final: 0 residues processed: 1028 average time/residue: 0.2090 time to fit residues: 320.4815 Evaluate side-chains 577 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 264 ASN A 362 HIS A 641 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 794 HIS A 849 ASN B 195 GLN B 281 HIS B 297 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 858 HIS D 192 GLN D 692 GLN D 806 ASN D 822 GLN E 309 HIS E 334 GLN E 361 HIS E 567 HIS E 688 ASN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 195 GLN F 297 ASN F 334 GLN F 726 GLN F 849 ASN ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104498 restraints weight = 68693.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.106979 restraints weight = 36859.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108591 restraints weight = 23745.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109598 restraints weight = 17654.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110105 restraints weight = 14632.449| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29005 Z= 0.182 Angle : 0.801 15.777 39185 Z= 0.400 Chirality : 0.049 0.287 4436 Planarity : 0.006 0.072 5114 Dihedral : 10.300 150.082 4163 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.85 % Allowed : 10.68 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.13), residues: 3532 helix: -0.88 (0.11), residues: 1950 sheet: -2.82 (0.24), residues: 398 loop : -2.24 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 669 TYR 0.028 0.002 TYR F 783 PHE 0.033 0.002 PHE C 729 TRP 0.025 0.003 TRP C 462 HIS 0.009 0.001 HIS F 747 Details of bonding type rmsd covalent geometry : bond 0.00410 (28988) covalent geometry : angle 0.80138 (39185) hydrogen bonds : bond 0.05769 ( 1422) hydrogen bonds : angle 5.96574 ( 4203) Misc. bond : bond 0.00295 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 633 time to evaluate : 0.968 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 169 THR cc_start: 0.6567 (p) cc_final: 0.6326 (p) REVERT: A 170 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7770 (pp20) REVERT: B 401 ILE cc_start: 0.7283 (mm) cc_final: 0.6130 (mt) REVERT: C 282 THR cc_start: 0.6913 (m) cc_final: 0.6539 (p) REVERT: C 293 MET cc_start: 0.6913 (mmm) cc_final: 0.6119 (mmm) REVERT: C 340 GLU cc_start: 0.6071 (pm20) cc_final: 0.5598 (pt0) REVERT: C 347 ILE cc_start: 0.5450 (mt) cc_final: 0.5032 (mt) REVERT: C 641 HIS cc_start: 0.5219 (OUTLIER) cc_final: 0.4742 (m-70) REVERT: D 305 ARG cc_start: 0.6838 (mmm160) cc_final: 0.6540 (ptp-170) REVERT: D 368 PRO cc_start: 0.6104 (Cg_exo) cc_final: 0.5854 (Cg_endo) REVERT: D 459 GLU cc_start: 0.5546 (tt0) cc_final: 0.5155 (tp30) REVERT: E 242 MET cc_start: 0.6283 (mmp) cc_final: 0.6074 (mmp) REVERT: E 568 HIS cc_start: 0.6949 (m-70) cc_final: 0.6656 (m90) REVERT: E 636 GLU cc_start: 0.5286 (pt0) cc_final: 0.4910 (pp20) REVERT: F 165 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6480 (m) REVERT: F 178 ASP cc_start: 0.6947 (m-30) cc_final: 0.6310 (p0) REVERT: F 186 GLU cc_start: 0.6185 (mp0) cc_final: 0.5296 (mt-10) REVERT: F 293 MET cc_start: 0.5663 (tpt) cc_final: 0.5412 (tpt) REVERT: F 314 THR cc_start: 0.6300 (t) cc_final: 0.3768 (p) REVERT: F 399 SER cc_start: 0.5471 (m) cc_final: 0.5209 (p) REVERT: F 626 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.5837 (t0) outliers start: 85 outliers final: 38 residues processed: 678 average time/residue: 0.1883 time to fit residues: 198.8050 Evaluate side-chains 510 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 469 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 812 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 201 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 281 HIS ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 574 ASN E 806 ASN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101591 restraints weight = 70417.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104025 restraints weight = 38514.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.105521 restraints weight = 25064.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106569 restraints weight = 18855.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107049 restraints weight = 15641.354| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 29005 Z= 0.264 Angle : 0.889 15.896 39185 Z= 0.443 Chirality : 0.050 0.317 4436 Planarity : 0.007 0.099 5114 Dihedral : 9.925 154.810 4163 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 3.96 % Allowed : 13.73 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.13), residues: 3532 helix: -0.51 (0.11), residues: 1980 sheet: -2.44 (0.25), residues: 385 loop : -1.99 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 561 TYR 0.027 0.002 TYR A 251 PHE 0.032 0.003 PHE B 729 TRP 0.031 0.002 TRP C 462 HIS 0.030 0.002 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00592 (28988) covalent geometry : angle 0.88944 (39185) hydrogen bonds : bond 0.05727 ( 1422) hydrogen bonds : angle 5.80614 ( 4203) Misc. bond : bond 0.01211 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 628 time to evaluate : 1.033 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: A 169 THR cc_start: 0.7726 (p) cc_final: 0.7522 (p) REVERT: A 184 ASP cc_start: 0.6251 (p0) cc_final: 0.5721 (t70) REVERT: A 207 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6107 (mt-10) REVERT: A 298 MET cc_start: 0.5023 (tpt) cc_final: 0.4775 (tpt) REVERT: A 552 MET cc_start: 0.5334 (mmp) cc_final: 0.4417 (ppp) REVERT: A 783 TYR cc_start: 0.6696 (m-10) cc_final: 0.6476 (m-80) REVERT: A 817 LEU cc_start: 0.8516 (tp) cc_final: 0.8205 (tt) REVERT: B 181 ILE cc_start: 0.7937 (mp) cc_final: 0.7720 (mt) REVERT: B 759 GLU cc_start: 0.6366 (tp30) cc_final: 0.6138 (tp30) REVERT: C 293 MET cc_start: 0.7424 (mmm) cc_final: 0.6503 (mmm) REVERT: D 293 MET cc_start: 0.2611 (tpt) cc_final: 0.2167 (mmt) REVERT: D 298 MET cc_start: 0.4865 (mtp) cc_final: 0.4637 (mtp) REVERT: D 622 MET cc_start: 0.4570 (ptp) cc_final: 0.4235 (ptt) REVERT: D 676 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7871 (tt) REVERT: E 299 LEU cc_start: 0.8157 (tt) cc_final: 0.7883 (pp) REVERT: E 731 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5272 (mp0) REVERT: F 165 THR cc_start: 0.6625 (OUTLIER) cc_final: 0.6374 (m) REVERT: F 167 ASP cc_start: 0.7014 (t0) cc_final: 0.6794 (t0) REVERT: F 186 GLU cc_start: 0.6755 (mp0) cc_final: 0.5709 (mt-10) REVERT: F 293 MET cc_start: 0.5437 (tpt) cc_final: 0.5218 (tpt) REVERT: F 297 ASN cc_start: 0.7208 (m-40) cc_final: 0.6699 (m-40) REVERT: F 399 SER cc_start: 0.5726 (m) cc_final: 0.5401 (p) REVERT: F 626 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.5936 (t0) REVERT: F 737 MET cc_start: 0.3891 (mmm) cc_final: 0.3284 (mmm) REVERT: F 846 LEU cc_start: 0.7002 (tt) cc_final: 0.6771 (tp) outliers start: 118 outliers final: 57 residues processed: 697 average time/residue: 0.1814 time to fit residues: 197.6124 Evaluate side-chains 553 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 491 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 723 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 731 GLU Chi-restraints excluded: chain E residue 744 VAL Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 707 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 262 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 204 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 190 optimal weight: 0.0000 chunk 259 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 281 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN B 195 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 831 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN F 857 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104507 restraints weight = 70031.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106973 restraints weight = 39155.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108534 restraints weight = 25628.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109588 restraints weight = 19246.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110149 restraints weight = 15894.605| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29005 Z= 0.149 Angle : 0.744 17.764 39185 Z= 0.367 Chirality : 0.046 0.313 4436 Planarity : 0.005 0.055 5114 Dihedral : 9.482 156.469 4163 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.32 % Allowed : 17.33 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3532 helix: 0.01 (0.11), residues: 1965 sheet: -2.29 (0.24), residues: 391 loop : -1.71 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 750 TYR 0.024 0.002 TYR D 734 PHE 0.026 0.002 PHE B 276 TRP 0.036 0.002 TRP C 462 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00315 (28988) covalent geometry : angle 0.74419 (39185) hydrogen bonds : bond 0.04879 ( 1422) hydrogen bonds : angle 5.46582 ( 4203) Misc. bond : bond 0.00327 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 534 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.7686 (p) cc_final: 0.7429 (p) REVERT: A 552 MET cc_start: 0.5402 (mmp) cc_final: 0.4370 (pmm) REVERT: A 622 MET cc_start: 0.7622 (ppp) cc_final: 0.6848 (ppp) REVERT: A 763 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5969 (m-10) REVERT: A 817 LEU cc_start: 0.8601 (tp) cc_final: 0.8286 (tt) REVERT: A 819 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5153 (ttt180) REVERT: B 585 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6065 (mtm-85) REVERT: B 715 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 293 MET cc_start: 0.7219 (mmm) cc_final: 0.6298 (mmm) REVERT: C 416 ASP cc_start: 0.7612 (t0) cc_final: 0.7396 (t0) REVERT: C 641 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.6360 (m90) REVERT: D 368 PRO cc_start: 0.7584 (Cg_exo) cc_final: 0.7307 (Cg_endo) REVERT: D 396 GLU cc_start: 0.4637 (tp30) cc_final: 0.4415 (tp30) REVERT: D 551 MET cc_start: 0.5329 (mpp) cc_final: 0.5124 (mtm) REVERT: D 675 LEU cc_start: 0.7674 (tp) cc_final: 0.7363 (tp) REVERT: D 771 ILE cc_start: 0.7080 (pt) cc_final: 0.6819 (mt) REVERT: E 171 ARG cc_start: 0.7450 (ptm160) cc_final: 0.6868 (ttp-110) REVERT: E 195 GLN cc_start: 0.7919 (pt0) cc_final: 0.7714 (tm-30) REVERT: E 299 LEU cc_start: 0.8248 (tt) cc_final: 0.8019 (pp) REVERT: E 551 MET cc_start: 0.5423 (mmp) cc_final: 0.5219 (mmp) REVERT: E 636 GLU cc_start: 0.7243 (pt0) cc_final: 0.6704 (pp20) REVERT: E 637 PHE cc_start: 0.5605 (m-10) cc_final: 0.4648 (m-10) REVERT: F 165 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.6317 (m) REVERT: F 186 GLU cc_start: 0.6511 (mp0) cc_final: 0.5452 (mt-10) REVERT: F 293 MET cc_start: 0.5240 (tpt) cc_final: 0.5007 (tpt) REVERT: F 297 ASN cc_start: 0.7178 (m-40) cc_final: 0.6618 (m-40) REVERT: F 314 THR cc_start: 0.6689 (t) cc_final: 0.5942 (m) REVERT: F 626 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.5871 (t0) outliers start: 99 outliers final: 56 residues processed: 594 average time/residue: 0.1599 time to fit residues: 155.7706 Evaluate side-chains 534 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 472 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 778 GLN Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 ASN Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 812 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 351 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 279 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 77 optimal weight: 0.0670 chunk 114 optimal weight: 0.4980 chunk 329 optimal weight: 10.0000 chunk 286 optimal weight: 0.0030 chunk 12 optimal weight: 4.9990 overall best weight: 1.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 269 GLN C 272 ASN C 595 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 GLN E 806 ASN E 824 GLN F 192 GLN F 692 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103733 restraints weight = 70116.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106140 restraints weight = 39569.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107718 restraints weight = 26105.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108702 restraints weight = 19697.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109381 restraints weight = 16388.532| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29005 Z= 0.149 Angle : 0.727 14.491 39185 Z= 0.356 Chirality : 0.046 0.188 4436 Planarity : 0.005 0.054 5114 Dihedral : 9.252 154.911 4163 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.22 % Allowed : 18.44 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3532 helix: 0.20 (0.12), residues: 1965 sheet: -2.02 (0.24), residues: 406 loop : -1.66 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 756 TYR 0.024 0.001 TYR F 322 PHE 0.024 0.002 PHE D 709 TRP 0.033 0.002 TRP C 462 HIS 0.011 0.001 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00330 (28988) covalent geometry : angle 0.72700 (39185) hydrogen bonds : bond 0.04728 ( 1422) hydrogen bonds : angle 5.38065 ( 4203) Misc. bond : bond 0.00366 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 517 time to evaluate : 1.105 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 169 THR cc_start: 0.7862 (p) cc_final: 0.7607 (p) REVERT: A 552 MET cc_start: 0.5486 (mmp) cc_final: 0.4385 (pmm) REVERT: A 622 MET cc_start: 0.7613 (ppp) cc_final: 0.7321 (ppp) REVERT: A 817 LEU cc_start: 0.8650 (tp) cc_final: 0.8408 (tt) REVERT: B 387 PRO cc_start: 0.8841 (Cg_endo) cc_final: 0.8520 (Cg_exo) REVERT: B 535 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7354 (mt-10) REVERT: B 634 MET cc_start: 0.6412 (mmm) cc_final: 0.6140 (tpt) REVERT: B 693 VAL cc_start: 0.8344 (t) cc_final: 0.8123 (t) REVERT: C 293 MET cc_start: 0.7571 (mmm) cc_final: 0.6585 (mmm) REVERT: C 317 ASP cc_start: 0.6711 (t0) cc_final: 0.6285 (t0) REVERT: C 535 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 641 HIS cc_start: 0.6821 (OUTLIER) cc_final: 0.6517 (m90) REVERT: D 212 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7843 (mmtm) REVERT: D 293 MET cc_start: 0.1917 (tpt) cc_final: 0.1627 (mmt) REVERT: D 368 PRO cc_start: 0.7567 (Cg_exo) cc_final: 0.7273 (Cg_endo) REVERT: D 675 LEU cc_start: 0.7928 (tp) cc_final: 0.7598 (tp) REVERT: D 771 ILE cc_start: 0.7313 (pt) cc_final: 0.7077 (mt) REVERT: E 551 MET cc_start: 0.5362 (mmp) cc_final: 0.5151 (mmp) REVERT: E 636 GLU cc_start: 0.7159 (pt0) cc_final: 0.6354 (pp20) REVERT: F 165 THR cc_start: 0.6634 (OUTLIER) cc_final: 0.6306 (m) REVERT: F 186 GLU cc_start: 0.6591 (mp0) cc_final: 0.5589 (mt-10) REVERT: F 575 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7118 (pm20) REVERT: F 626 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.5894 (t0) REVERT: F 737 MET cc_start: 0.3830 (mmm) cc_final: 0.3442 (mmm) REVERT: F 846 LEU cc_start: 0.7059 (tt) cc_final: 0.6774 (tp) outliers start: 96 outliers final: 55 residues processed: 577 average time/residue: 0.1674 time to fit residues: 156.8097 Evaluate side-chains 521 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 462 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 744 VAL Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 96 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 175 optimal weight: 0.0980 chunk 222 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 349 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 806 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 849 ASN F 361 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.128624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104784 restraints weight = 69754.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107179 restraints weight = 38876.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108675 restraints weight = 25729.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109719 restraints weight = 19510.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110238 restraints weight = 16262.204| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29005 Z= 0.134 Angle : 0.705 14.160 39185 Z= 0.343 Chirality : 0.045 0.239 4436 Planarity : 0.005 0.062 5114 Dihedral : 9.117 154.516 4163 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.82 % Allowed : 20.35 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3532 helix: 0.36 (0.12), residues: 1969 sheet: -1.87 (0.24), residues: 405 loop : -1.55 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 258 TYR 0.017 0.001 TYR F 322 PHE 0.019 0.002 PHE E 749 TRP 0.031 0.002 TRP C 462 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00290 (28988) covalent geometry : angle 0.70517 (39185) hydrogen bonds : bond 0.04501 ( 1422) hydrogen bonds : angle 5.25228 ( 4203) Misc. bond : bond 0.00206 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 509 time to evaluate : 1.086 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 169 THR cc_start: 0.7834 (p) cc_final: 0.7535 (p) REVERT: A 174 GLN cc_start: 0.8424 (mt0) cc_final: 0.8088 (pt0) REVERT: A 763 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: A 817 LEU cc_start: 0.8642 (tp) cc_final: 0.8410 (tt) REVERT: B 387 PRO cc_start: 0.8883 (Cg_endo) cc_final: 0.8530 (Cg_exo) REVERT: B 634 MET cc_start: 0.6468 (mmm) cc_final: 0.6255 (tpt) REVERT: B 690 LEU cc_start: 0.8255 (mt) cc_final: 0.8051 (mt) REVERT: C 293 MET cc_start: 0.7699 (mmm) cc_final: 0.6623 (mmm) REVERT: C 317 ASP cc_start: 0.6391 (t0) cc_final: 0.5957 (t0) REVERT: C 455 TYR cc_start: 0.6810 (t80) cc_final: 0.6563 (t80) REVERT: C 535 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 565 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 822 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7578 (pt0) REVERT: D 212 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7374 (mmtm) REVERT: D 368 PRO cc_start: 0.7588 (Cg_exo) cc_final: 0.7272 (Cg_endo) REVERT: D 551 MET cc_start: 0.5165 (mtm) cc_final: 0.4951 (mtm) REVERT: E 637 PHE cc_start: 0.6151 (m-10) cc_final: 0.5631 (m-10) REVERT: F 165 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6319 (m) REVERT: F 186 GLU cc_start: 0.6700 (mp0) cc_final: 0.5644 (mt-10) REVERT: F 325 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8611 (mptt) REVERT: F 354 LYS cc_start: 0.6371 (tttt) cc_final: 0.5804 (ptmt) REVERT: F 535 GLU cc_start: 0.7483 (tp30) cc_final: 0.7174 (tp30) REVERT: F 616 LYS cc_start: 0.7670 (mmtm) cc_final: 0.6375 (pttm) REVERT: F 626 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5812 (t0) REVERT: F 846 LEU cc_start: 0.7249 (tt) cc_final: 0.7012 (tp) outliers start: 84 outliers final: 59 residues processed: 562 average time/residue: 0.1597 time to fit residues: 146.4731 Evaluate side-chains 533 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 470 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 620 ASN Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 852 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 216 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 219 optimal weight: 0.2980 chunk 281 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 426 GLN C 595 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 HIS F 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103949 restraints weight = 69516.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106291 restraints weight = 39230.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107812 restraints weight = 26114.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108733 restraints weight = 19804.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109381 restraints weight = 16683.238| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29005 Z= 0.146 Angle : 0.724 22.422 39185 Z= 0.354 Chirality : 0.045 0.209 4436 Planarity : 0.005 0.054 5114 Dihedral : 9.084 153.801 4163 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.26 % Allowed : 20.38 % Favored : 76.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3532 helix: 0.45 (0.12), residues: 1979 sheet: -1.80 (0.24), residues: 403 loop : -1.44 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 320 TYR 0.021 0.001 TYR B 164 PHE 0.027 0.002 PHE D 333 TRP 0.033 0.002 TRP C 462 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00323 (28988) covalent geometry : angle 0.72423 (39185) hydrogen bonds : bond 0.04493 ( 1422) hydrogen bonds : angle 5.21420 ( 4203) Misc. bond : bond 0.00307 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 518 time to evaluate : 1.009 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 169 THR cc_start: 0.7836 (p) cc_final: 0.7562 (p) REVERT: A 622 MET cc_start: 0.7621 (ppp) cc_final: 0.7294 (ppp) REVERT: A 712 THR cc_start: 0.7285 (p) cc_final: 0.7022 (p) REVERT: A 745 VAL cc_start: 0.8079 (t) cc_final: 0.7801 (p) REVERT: A 763 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: A 817 LEU cc_start: 0.8617 (tp) cc_final: 0.8382 (tt) REVERT: B 585 ARG cc_start: 0.6835 (mtt-85) cc_final: 0.5977 (mtm-85) REVERT: B 603 PHE cc_start: 0.7877 (m-10) cc_final: 0.7671 (m-10) REVERT: B 634 MET cc_start: 0.6726 (mmm) cc_final: 0.6478 (tpt) REVERT: B 774 ILE cc_start: 0.7788 (pt) cc_final: 0.7586 (pt) REVERT: C 293 MET cc_start: 0.7841 (mmm) cc_final: 0.6478 (mmm) REVERT: C 317 ASP cc_start: 0.6837 (t0) cc_final: 0.6314 (t0) REVERT: C 565 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7686 (mm-30) REVERT: C 754 ILE cc_start: 0.8087 (pt) cc_final: 0.7486 (mt) REVERT: C 822 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7637 (pt0) REVERT: C 847 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6527 (mm-30) REVERT: D 212 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7447 (mmtm) REVERT: D 368 PRO cc_start: 0.7755 (Cg_exo) cc_final: 0.7468 (Cg_endo) REVERT: D 691 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7271 (tt) REVERT: D 695 ASP cc_start: 0.6296 (t0) cc_final: 0.6014 (t0) REVERT: D 729 PHE cc_start: 0.6838 (t80) cc_final: 0.6550 (t80) REVERT: E 551 MET cc_start: 0.5078 (mmp) cc_final: 0.4849 (mmp) REVERT: E 646 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6888 (tt) REVERT: F 165 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6341 (m) REVERT: F 186 GLU cc_start: 0.7050 (mp0) cc_final: 0.6017 (mt-10) REVERT: F 325 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8650 (mptt) REVERT: F 616 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7502 (mmtt) REVERT: F 626 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.5940 (t0) outliers start: 97 outliers final: 63 residues processed: 580 average time/residue: 0.1610 time to fit residues: 152.3917 Evaluate side-chains 537 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 468 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 852 ARG Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 839 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 44 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS C 806 ASN D 281 HIS D 711 ASN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN E 857 GLN F 159 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN F 806 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.125390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101384 restraints weight = 70716.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103569 restraints weight = 41067.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104989 restraints weight = 27984.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105912 restraints weight = 21644.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106401 restraints weight = 18356.888| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29005 Z= 0.190 Angle : 0.799 17.652 39185 Z= 0.398 Chirality : 0.049 0.342 4436 Planarity : 0.006 0.078 5114 Dihedral : 9.167 152.158 4163 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.26 % Allowed : 21.66 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3532 helix: 0.29 (0.12), residues: 1984 sheet: -1.75 (0.24), residues: 409 loop : -1.39 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 258 TYR 0.032 0.002 TYR B 671 PHE 0.044 0.002 PHE E 276 TRP 0.036 0.002 TRP C 462 HIS 0.011 0.002 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00427 (28988) covalent geometry : angle 0.79881 (39185) hydrogen bonds : bond 0.04871 ( 1422) hydrogen bonds : angle 5.32933 ( 4203) Misc. bond : bond 0.00446 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 561 time to evaluate : 0.990 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 169 THR cc_start: 0.8308 (p) cc_final: 0.8029 (p) REVERT: A 391 ILE cc_start: 0.8177 (mm) cc_final: 0.7587 (tp) REVERT: A 533 ASP cc_start: 0.7142 (p0) cc_final: 0.6746 (t0) REVERT: A 622 MET cc_start: 0.7933 (ppp) cc_final: 0.7636 (ppp) REVERT: A 696 ASP cc_start: 0.7262 (m-30) cc_final: 0.7004 (t0) REVERT: B 276 PHE cc_start: 0.7807 (t80) cc_final: 0.7542 (t80) REVERT: B 603 PHE cc_start: 0.8048 (m-10) cc_final: 0.7792 (m-80) REVERT: B 692 GLN cc_start: 0.7878 (mt0) cc_final: 0.7668 (mt0) REVERT: C 317 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6893 (t0) REVERT: C 562 MET cc_start: 0.8006 (tpp) cc_final: 0.7772 (tpp) REVERT: C 766 LEU cc_start: 0.7439 (mt) cc_final: 0.7201 (mt) REVERT: C 806 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8055 (t0) REVERT: C 822 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7941 (pt0) REVERT: D 368 PRO cc_start: 0.8145 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: D 634 MET cc_start: 0.8705 (ttm) cc_final: 0.8462 (ttm) REVERT: D 637 PHE cc_start: 0.8400 (m-80) cc_final: 0.8083 (m-10) REVERT: D 644 SER cc_start: 0.7969 (m) cc_final: 0.7744 (p) REVERT: D 675 LEU cc_start: 0.8714 (tp) cc_final: 0.8004 (tp) REVERT: E 322 TYR cc_start: 0.7460 (m-80) cc_final: 0.7123 (m-80) REVERT: E 396 GLU cc_start: 0.7588 (tt0) cc_final: 0.7262 (tt0) REVERT: E 638 MET cc_start: 0.7948 (tpt) cc_final: 0.6924 (mmt) REVERT: E 708 ASP cc_start: 0.6207 (t0) cc_final: 0.5197 (p0) REVERT: E 809 ASP cc_start: 0.7764 (t0) cc_final: 0.6743 (m-30) REVERT: F 293 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.4840 (tpt) REVERT: F 325 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8534 (mmtm) REVERT: F 616 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7429 (mmtp) REVERT: F 626 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5726 (t0) outliers start: 97 outliers final: 67 residues processed: 619 average time/residue: 0.1643 time to fit residues: 163.5354 Evaluate side-chains 525 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 454 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 852 ARG Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 839 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 287 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN C 806 ASN C 857 GLN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102316 restraints weight = 70771.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104691 restraints weight = 42925.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106345 restraints weight = 28366.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106523 restraints weight = 20407.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106685 restraints weight = 20413.659| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 1.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29005 Z= 0.143 Angle : 0.763 15.165 39185 Z= 0.371 Chirality : 0.047 0.245 4436 Planarity : 0.005 0.059 5114 Dihedral : 8.958 149.967 4163 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.52 % Allowed : 23.61 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3532 helix: 0.49 (0.12), residues: 1965 sheet: -1.63 (0.24), residues: 401 loop : -1.34 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 320 TYR 0.019 0.001 TYR A 783 PHE 0.019 0.002 PHE B 276 TRP 0.038 0.002 TRP C 462 HIS 0.012 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00316 (28988) covalent geometry : angle 0.76277 (39185) hydrogen bonds : bond 0.04527 ( 1422) hydrogen bonds : angle 5.22146 ( 4203) Misc. bond : bond 0.00268 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 508 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.8281 (p) cc_final: 0.7981 (p) REVERT: A 320 ARG cc_start: 0.7405 (ttm170) cc_final: 0.6957 (ttm170) REVERT: A 391 ILE cc_start: 0.8115 (mm) cc_final: 0.7580 (tp) REVERT: A 533 ASP cc_start: 0.7402 (p0) cc_final: 0.6768 (t0) REVERT: A 696 ASP cc_start: 0.7424 (m-30) cc_final: 0.7051 (m-30) REVERT: A 763 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: B 325 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7345 (mmtt) REVERT: B 692 GLN cc_start: 0.7707 (mt0) cc_final: 0.7342 (mt0) REVERT: C 562 MET cc_start: 0.8043 (tpp) cc_final: 0.7672 (tpp) REVERT: C 677 ASP cc_start: 0.7907 (t0) cc_final: 0.7033 (p0) REVERT: C 800 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8199 (mt) REVERT: C 806 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7993 (t0) REVERT: C 822 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7677 (pt0) REVERT: D 368 PRO cc_start: 0.8127 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: D 634 MET cc_start: 0.8583 (ttm) cc_final: 0.8378 (ttm) REVERT: D 637 PHE cc_start: 0.8457 (m-80) cc_final: 0.8223 (m-10) REVERT: D 644 SER cc_start: 0.7950 (m) cc_final: 0.7695 (p) REVERT: D 675 LEU cc_start: 0.8656 (tp) cc_final: 0.7939 (tp) REVERT: D 676 LEU cc_start: 0.8411 (tt) cc_final: 0.6967 (tt) REVERT: D 691 LEU cc_start: 0.8356 (tt) cc_final: 0.8131 (tp) REVERT: D 695 ASP cc_start: 0.6797 (t0) cc_final: 0.6174 (t0) REVERT: D 696 ASP cc_start: 0.7720 (m-30) cc_final: 0.7253 (m-30) REVERT: E 322 TYR cc_start: 0.7434 (m-80) cc_final: 0.7023 (m-80) REVERT: E 638 MET cc_start: 0.7743 (tpt) cc_final: 0.7541 (mmt) REVERT: E 646 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7419 (tt) REVERT: E 708 ASP cc_start: 0.6385 (t0) cc_final: 0.5264 (p0) REVERT: E 737 MET cc_start: 0.5738 (mmm) cc_final: 0.4813 (mtt) REVERT: E 809 ASP cc_start: 0.7728 (t0) cc_final: 0.6633 (m-30) REVERT: F 186 GLU cc_start: 0.7969 (mp0) cc_final: 0.5874 (mt-10) REVERT: F 293 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.4649 (tpt) REVERT: F 325 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8595 (mmtm) REVERT: F 626 ASP cc_start: 0.5995 (OUTLIER) cc_final: 0.5409 (t0) REVERT: F 638 MET cc_start: 0.5478 (mmm) cc_final: 0.4951 (mmm) REVERT: F 639 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7237 (mp0) outliers start: 75 outliers final: 52 residues processed: 553 average time/residue: 0.1560 time to fit residues: 141.8230 Evaluate side-chains 517 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 459 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 806 ASN Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 16 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 283 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 289 optimal weight: 0.9990 chunk 353 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 822 GLN F 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096988 restraints weight = 71539.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099184 restraints weight = 41582.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100616 restraints weight = 28256.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101561 restraints weight = 21745.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101992 restraints weight = 18350.001| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 1.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 29005 Z= 0.247 Angle : 0.936 24.825 39185 Z= 0.467 Chirality : 0.052 0.264 4436 Planarity : 0.007 0.101 5114 Dihedral : 9.479 155.613 4163 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.72 % Allowed : 24.31 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3532 helix: -0.04 (0.11), residues: 1964 sheet: -1.80 (0.24), residues: 387 loop : -1.37 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 852 TYR 0.024 0.003 TYR E 656 PHE 0.083 0.003 PHE A 749 TRP 0.049 0.003 TRP C 462 HIS 0.014 0.002 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00572 (28988) covalent geometry : angle 0.93566 (39185) hydrogen bonds : bond 0.05403 ( 1422) hydrogen bonds : angle 5.66253 ( 4203) Misc. bond : bond 0.00306 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 512 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 217 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8009 (mt-10) REVERT: A 320 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7822 (ttm170) REVERT: A 598 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8563 (mt) REVERT: A 696 ASP cc_start: 0.7893 (m-30) cc_final: 0.7533 (m-30) REVERT: A 819 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5531 (ttt180) REVERT: B 162 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7164 (tmmt) REVERT: B 293 MET cc_start: 0.8315 (tpp) cc_final: 0.7700 (tpp) REVERT: B 325 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7678 (mmtt) REVERT: B 558 LYS cc_start: 0.7884 (tppt) cc_final: 0.7591 (mmmt) REVERT: B 637 PHE cc_start: 0.7604 (m-10) cc_final: 0.7269 (m-10) REVERT: B 692 GLN cc_start: 0.8059 (mt0) cc_final: 0.7710 (mt0) REVERT: B 701 ASP cc_start: 0.7498 (p0) cc_final: 0.7141 (p0) REVERT: C 562 MET cc_start: 0.8260 (tpp) cc_final: 0.8018 (tpp) REVERT: C 642 SER cc_start: 0.8557 (p) cc_final: 0.8302 (t) REVERT: C 705 ARG cc_start: 0.7921 (ptt90) cc_final: 0.7484 (ptp90) REVERT: C 742 LEU cc_start: 0.8701 (tp) cc_final: 0.8493 (tt) REVERT: C 780 LYS cc_start: 0.8677 (mttp) cc_final: 0.8384 (mmtm) REVERT: D 240 LEU cc_start: 0.7734 (pp) cc_final: 0.7480 (pp) REVERT: D 535 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6588 (mm-30) REVERT: D 581 SER cc_start: 0.7970 (m) cc_final: 0.7560 (p) REVERT: D 691 LEU cc_start: 0.8688 (tt) cc_final: 0.8446 (tp) REVERT: D 695 ASP cc_start: 0.6833 (t0) cc_final: 0.6287 (t0) REVERT: D 696 ASP cc_start: 0.7904 (m-30) cc_final: 0.7639 (m-30) REVERT: E 353 LEU cc_start: 0.8454 (mm) cc_final: 0.7940 (mm) REVERT: E 620 ASN cc_start: 0.7251 (m-40) cc_final: 0.6883 (m-40) REVERT: E 708 ASP cc_start: 0.6924 (t0) cc_final: 0.5935 (p0) REVERT: E 737 MET cc_start: 0.5989 (mmm) cc_final: 0.4915 (mtt) REVERT: E 826 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: F 293 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5050 (tpt) REVERT: F 325 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8445 (mmtm) REVERT: F 616 LYS cc_start: 0.7330 (mmtm) cc_final: 0.6376 (pttt) REVERT: F 638 MET cc_start: 0.6163 (mmm) cc_final: 0.5282 (mmm) outliers start: 81 outliers final: 56 residues processed: 558 average time/residue: 0.1643 time to fit residues: 148.6368 Evaluate side-chains 504 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 442 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 620 ASN Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 825 ILE Chi-restraints excluded: chain F residue 839 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 350 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 335 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 316 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 281 HIS ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN E 200 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 822 GLN F 692 GLN F 824 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.124044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100312 restraints weight = 71294.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102446 restraints weight = 41622.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103883 restraints weight = 28440.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104677 restraints weight = 21893.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105349 restraints weight = 18686.488| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 1.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29005 Z= 0.157 Angle : 0.825 14.523 39185 Z= 0.403 Chirality : 0.049 0.294 4436 Planarity : 0.005 0.057 5114 Dihedral : 9.135 155.520 4163 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.08 % Allowed : 25.25 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3532 helix: 0.28 (0.12), residues: 1959 sheet: -1.75 (0.24), residues: 398 loop : -1.27 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 698 TYR 0.025 0.002 TYR D 322 PHE 0.023 0.002 PHE A 749 TRP 0.035 0.002 TRP C 462 HIS 0.038 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00351 (28988) covalent geometry : angle 0.82538 (39185) hydrogen bonds : bond 0.04663 ( 1422) hydrogen bonds : angle 5.34125 ( 4203) Misc. bond : bond 0.00264 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5297.90 seconds wall clock time: 92 minutes 2.30 seconds (5522.30 seconds total)