Starting phenix.real_space_refine on Mon Sep 14 08:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qs6_4624/09_2026/6qs6_4624.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs6_4624/09_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_4624/09_2026/6qs6_4624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs6_4624/09_2026/6qs6_4624.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qs6_4624/09_2026/6qs6_4624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qs6_4624/09_2026/6qs6_4624.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qs6_4624/09_2026/6qs6_4624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs6_4624/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.73, per 1000 atoms: 0.20 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 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: 0.90 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: 5.39 Time building geometry restraints manager: 2.91 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: 17558 32.10 - 64.19: 183 64.19 - 96.29: 17 96.29 - 128.39: 2 128.39 - 160.48: 2 Dihedral angle restraints: 17762 sinusoidal: 7445 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 17759 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 23.890 Find NCS groups from input model: 0.770 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4566 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 : 10.530 160.483 11110 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/Z covalent geometry : bond 0.01070 / 0.44 (28988) covalent geometry : angle 1.09030 / 0.58 (39185) hydrogen bonds : bond 0.16865 / 11.26 ( 1422) hydrogen bonds : angle 7.91422 / 5.65 ( 4203) Misc. bond : bond 0.00510 / 0.36 ( 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 : 1.141 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: 0.2322 time to fit residues: 358.8549 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 : 1.103 ------------------------------------------------------------------------------- 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... A 195 GLN A 264 ASN 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 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104527 restraints weight = 69032.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107012 restraints weight = 37217.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108634 restraints weight = 24038.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109657 restraints weight = 17983.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110237 restraints weight = 14962.975| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 29005 Z= 0.177 Angle : 0.799 15.612 39185 Z= 0.399 Chirality : 0.049 0.298 4436 Planarity : 0.006 0.068 5114 Dihedral : 8.821 149.584 4064 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 10.71 % Favored : 86.50 % 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: -2.45 (0.13), residues: 3532 helix: -0.88 (0.11), residues: 1955 sheet: -2.81 (0.24), residues: 398 loop : -2.23 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 669 TYR 0.029 0.002 TYR F 783 PHE 0.034 0.002 PHE C 729 TRP 0.025 0.002 TRP C 462 HIS 0.009 0.001 HIS F 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (28988) covalent geometry : angle 0.79910 / 0.40 (39185) hydrogen bonds : bond 0.05701 / 3.87 ( 1422) hydrogen bonds : angle 5.95162 / 4.20 ( 4203) Misc. bond : bond 0.00240 / 0.16 ( 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 719 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 636 time to evaluate : 1.205 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: A 169 THR cc_start: 0.6549 (p) cc_final: 0.6313 (p) REVERT: A 170 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7775 (pp20) REVERT: B 401 ILE cc_start: 0.7294 (mm) cc_final: 0.6143 (mt) REVERT: C 282 THR cc_start: 0.6970 (m) cc_final: 0.6573 (p) REVERT: C 293 MET cc_start: 0.6890 (mmm) cc_final: 0.6052 (mmm) REVERT: C 340 GLU cc_start: 0.6052 (pm20) cc_final: 0.5596 (pt0) REVERT: C 641 HIS cc_start: 0.5259 (OUTLIER) cc_final: 0.4791 (m-70) REVERT: C 780 LYS cc_start: 0.7864 (pttt) cc_final: 0.7570 (mttp) REVERT: D 305 ARG cc_start: 0.6835 (mmm160) cc_final: 0.6553 (ptp-170) REVERT: D 368 PRO cc_start: 0.6080 (Cg_exo) cc_final: 0.5823 (Cg_endo) REVERT: D 459 GLU cc_start: 0.5532 (tt0) cc_final: 0.5161 (tp30) REVERT: E 283 MET cc_start: 0.6250 (mtp) cc_final: 0.6039 (ptt) REVERT: E 568 HIS cc_start: 0.7081 (m-70) cc_final: 0.6787 (m90) REVERT: E 636 GLU cc_start: 0.5378 (pt0) cc_final: 0.5165 (pp20) REVERT: F 165 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6382 (m) REVERT: F 178 ASP cc_start: 0.6949 (m-30) cc_final: 0.6315 (p0) REVERT: F 186 GLU cc_start: 0.6193 (mp0) cc_final: 0.5309 (mt-10) REVERT: F 293 MET cc_start: 0.5654 (tpt) cc_final: 0.5438 (tpt) REVERT: F 314 THR cc_start: 0.6368 (t) cc_final: 0.3818 (p) REVERT: F 399 SER cc_start: 0.5501 (m) cc_final: 0.5289 (p) REVERT: F 616 LYS cc_start: 0.7894 (mttt) cc_final: 0.7692 (pttt) REVERT: F 626 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.5885 (t0) outliers start: 83 outliers final: 35 residues processed: 681 average time/residue: 0.2107 time to fit residues: 223.7856 Evaluate side-chains 505 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 467 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE 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 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 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: 0.9990 chunk 231 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 354 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 362 HIS ** 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 ** 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** D 192 GLN D 281 HIS E 334 GLN E 574 ASN E 849 ASN F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103271 restraints weight = 69957.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105874 restraints weight = 37493.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107552 restraints weight = 24036.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108463 restraints weight = 17716.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109232 restraints weight = 14810.086| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29005 Z= 0.181 Angle : 0.775 13.451 39185 Z= 0.384 Chirality : 0.047 0.244 4436 Planarity : 0.006 0.066 5114 Dihedral : 8.555 150.664 4064 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.79 % Allowed : 13.10 % Favored : 83.11 % 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: -1.73 (0.14), residues: 3532 helix: -0.25 (0.11), residues: 1979 sheet: -2.64 (0.25), residues: 390 loop : -1.97 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 356 TYR 0.016 0.001 TYR B 671 PHE 0.034 0.003 PHE B 729 TRP 0.031 0.002 TRP C 462 HIS 0.028 0.001 HIS C 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (28988) covalent geometry : angle 0.77536 / 0.38 (39185) hydrogen bonds : bond 0.05262 / 3.58 ( 1422) hydrogen bonds : angle 5.64516 / 3.98 ( 4203) Misc. bond : bond 0.00447 / 0.27 ( 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 699 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 586 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.7386 (p) cc_final: 0.7160 (p) REVERT: A 184 ASP cc_start: 0.6201 (p0) cc_final: 0.5958 (t70) REVERT: A 552 MET cc_start: 0.5402 (mmp) cc_final: 0.4353 (pmm) REVERT: A 562 MET cc_start: 0.6276 (tpp) cc_final: 0.6022 (tpt) REVERT: A 603 PHE cc_start: 0.5731 (m-10) cc_final: 0.5375 (m-10) REVERT: A 622 MET cc_start: 0.7775 (ppp) cc_final: 0.7382 (ppp) REVERT: A 783 TYR cc_start: 0.6703 (m-10) cc_final: 0.6487 (m-80) REVERT: A 817 LEU cc_start: 0.8423 (tp) cc_final: 0.8080 (tt) REVERT: B 181 ILE cc_start: 0.7178 (mp) cc_final: 0.6945 (mt) REVERT: B 326 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6922 (t0) REVERT: C 282 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7608 (p) REVERT: C 293 MET cc_start: 0.7034 (mmm) cc_final: 0.5935 (mmm) REVERT: C 340 GLU cc_start: 0.6587 (pm20) cc_final: 0.6179 (pt0) REVERT: C 614 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6687 (tp) REVERT: C 780 LYS cc_start: 0.8255 (pttt) cc_final: 0.7899 (mttp) REVERT: D 257 GLU cc_start: 0.6000 (tm-30) cc_final: 0.5734 (tm-30) REVERT: D 293 MET cc_start: 0.2642 (tpt) cc_final: 0.2176 (mmt) REVERT: D 298 MET cc_start: 0.4916 (mtp) cc_final: 0.4675 (mtp) REVERT: E 186 GLU cc_start: 0.6490 (mp0) cc_final: 0.6233 (mp0) REVERT: F 165 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6429 (m) REVERT: F 186 GLU cc_start: 0.6518 (mp0) cc_final: 0.5558 (mt-10) REVERT: F 297 ASN cc_start: 0.7226 (m-40) cc_final: 0.6682 (m-40) REVERT: F 399 SER cc_start: 0.5690 (m) cc_final: 0.5290 (p) REVERT: F 535 GLU cc_start: 0.7716 (tp30) cc_final: 0.7391 (tp30) REVERT: F 626 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.5962 (t0) REVERT: F 737 MET cc_start: 0.3500 (mmm) cc_final: 0.2987 (mmm) outliers start: 113 outliers final: 57 residues processed: 651 average time/residue: 0.1998 time to fit residues: 207.2088 Evaluate side-chains 542 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 480 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU 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 329 LEU Chi-restraints excluded: chain A residue 559 LEU 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 237 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 614 LEU 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 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 632 ILE Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 707 VAL 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 219 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 646 LEU Chi-restraints excluded: chain E residue 760 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 Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 812 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 262 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 204 optimal weight: 0.1980 chunk 228 optimal weight: 1.9990 chunk 277 optimal weight: 0.0970 chunk 348 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** 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** D 281 HIS D 321 GLN E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.105767 restraints weight = 69709.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108258 restraints weight = 38547.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109911 restraints weight = 25067.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.110957 restraints weight = 18613.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111625 restraints weight = 15357.655| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29005 Z= 0.143 Angle : 0.726 12.500 39185 Z= 0.355 Chirality : 0.046 0.234 4436 Planarity : 0.005 0.060 5114 Dihedral : 8.301 149.055 4064 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.36 % Allowed : 16.29 % Favored : 80.36 % 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: -1.24 (0.14), residues: 3532 helix: 0.10 (0.11), residues: 1963 sheet: -2.39 (0.24), residues: 393 loop : -1.65 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 351 TYR 0.018 0.001 TYR B 251 PHE 0.043 0.002 PHE B 621 TRP 0.036 0.002 TRP C 462 HIS 0.016 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (28988) covalent geometry : angle 0.72646 / 0.36 (39185) hydrogen bonds : bond 0.04819 / 3.25 ( 1422) hydrogen bonds : angle 5.41134 / 3.82 ( 4203) Misc. bond : bond 0.00619 / 0.40 ( 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 628 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 528 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.7469 (p) cc_final: 0.7193 (p) REVERT: A 174 GLN cc_start: 0.8066 (mt0) cc_final: 0.7789 (pt0) REVERT: A 552 MET cc_start: 0.5589 (mmp) cc_final: 0.4536 (pmm) REVERT: A 562 MET cc_start: 0.6420 (tpp) cc_final: 0.6152 (tpt) REVERT: A 603 PHE cc_start: 0.5730 (m-10) cc_final: 0.5301 (m-10) REVERT: A 622 MET cc_start: 0.7675 (ppp) cc_final: 0.7380 (ppp) REVERT: A 741 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6921 (p) REVERT: A 817 LEU cc_start: 0.8498 (tp) cc_final: 0.8246 (tt) REVERT: B 181 ILE cc_start: 0.7075 (mp) cc_final: 0.6837 (mt) REVERT: B 204 LEU cc_start: 0.8235 (mt) cc_final: 0.8008 (mp) REVERT: C 282 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7475 (p) REVERT: C 293 MET cc_start: 0.6985 (mmm) cc_final: 0.4668 (mmm) REVERT: C 340 GLU cc_start: 0.6377 (pm20) cc_final: 0.6013 (pt0) REVERT: C 780 LYS cc_start: 0.8116 (pttt) cc_final: 0.7892 (mttp) REVERT: C 815 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7865 (ttm110) REVERT: D 257 GLU cc_start: 0.6033 (tm-30) cc_final: 0.5783 (tm-30) REVERT: D 281 HIS cc_start: 0.4889 (OUTLIER) cc_final: 0.4332 (t70) REVERT: D 368 PRO cc_start: 0.7099 (Cg_exo) cc_final: 0.6884 (Cg_endo) REVERT: D 598 ILE cc_start: 0.8021 (mt) cc_final: 0.7419 (tp) REVERT: D 771 ILE cc_start: 0.6800 (pt) cc_final: 0.6582 (mt) REVERT: E 171 ARG cc_start: 0.7217 (ptm160) cc_final: 0.6814 (ttp-170) REVERT: E 186 GLU cc_start: 0.6413 (mp0) cc_final: 0.6169 (mp0) REVERT: E 242 MET cc_start: 0.5529 (mmp) cc_final: 0.5163 (mmp) REVERT: E 565 GLU cc_start: 0.6459 (pt0) cc_final: 0.6187 (pt0) REVERT: E 636 GLU cc_start: 0.6930 (pt0) cc_final: 0.6683 (pp20) REVERT: F 186 GLU cc_start: 0.6342 (mp0) cc_final: 0.5345 (mt-10) REVERT: F 399 SER cc_start: 0.5675 (m) cc_final: 0.5414 (p) REVERT: F 535 GLU cc_start: 0.7695 (tp30) cc_final: 0.7480 (tp30) REVERT: F 626 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.5812 (t0) outliers start: 100 outliers final: 59 residues processed: 592 average time/residue: 0.1729 time to fit residues: 166.9712 Evaluate side-chains 523 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 460 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 240 LEU 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 689 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 778 GLN 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 259 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 405 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 717 THR 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 282 THR Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 299 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 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 F residue 178 ASP 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 812 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 351 optimal weight: 0.4980 chunk 333 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 329 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 272 ASN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN E 269 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 849 ASN E 857 GLN F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102544 restraints weight = 70622.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104952 restraints weight = 39485.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106570 restraints weight = 26072.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107649 restraints weight = 19543.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108237 restraints weight = 16123.919| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29005 Z= 0.209 Angle : 0.797 25.720 39185 Z= 0.399 Chirality : 0.049 0.434 4436 Planarity : 0.006 0.092 5114 Dihedral : 8.349 157.627 4064 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.69 % Allowed : 17.26 % Favored : 79.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3532 helix: 0.11 (0.11), residues: 1979 sheet: -2.15 (0.24), residues: 402 loop : -1.63 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 756 TYR 0.026 0.002 TYR B 783 PHE 0.022 0.002 PHE B 276 TRP 0.036 0.002 TRP C 462 HIS 0.044 0.002 HIS C 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (28988) covalent geometry : angle 0.79722 / 0.40 (39185) hydrogen bonds : bond 0.05025 / 3.37 ( 1422) hydrogen bonds : angle 5.43439 / 3.82 ( 4203) Misc. bond : bond 0.00874 / 0.60 ( 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 670 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 560 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.7806 (p) cc_final: 0.7506 (p) REVERT: A 316 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6543 (tt) REVERT: A 622 MET cc_start: 0.7569 (ppp) cc_final: 0.7292 (ppp) REVERT: A 817 LEU cc_start: 0.8607 (tp) cc_final: 0.8368 (tt) REVERT: B 181 ILE cc_start: 0.8201 (mp) cc_final: 0.7995 (mt) REVERT: B 276 PHE cc_start: 0.7347 (t80) cc_final: 0.7104 (t80) REVERT: B 601 PHE cc_start: 0.7582 (m-80) cc_final: 0.7364 (m-80) REVERT: C 282 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8211 (t) REVERT: C 293 MET cc_start: 0.7922 (mmm) cc_final: 0.6994 (mmm) REVERT: C 298 MET cc_start: 0.8374 (mpp) cc_final: 0.8000 (mpp) REVERT: C 847 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7040 (mm-30) REVERT: D 257 GLU cc_start: 0.6379 (tm-30) cc_final: 0.6082 (tm-30) REVERT: D 293 MET cc_start: 0.2084 (tpt) cc_final: 0.1736 (mmt) REVERT: D 368 PRO cc_start: 0.7611 (Cg_exo) cc_final: 0.7275 (Cg_endo) REVERT: D 384 ARG cc_start: 0.6954 (mmt90) cc_final: 0.6525 (mmt90) REVERT: D 716 MET cc_start: 0.7366 (ptp) cc_final: 0.7132 (ptm) REVERT: D 771 ILE cc_start: 0.7348 (pt) cc_final: 0.7129 (mt) REVERT: E 186 GLU cc_start: 0.6452 (mp0) cc_final: 0.6175 (mp0) REVERT: E 195 GLN cc_start: 0.7928 (pt0) cc_final: 0.7663 (tm-30) REVERT: E 242 MET cc_start: 0.5818 (mmp) cc_final: 0.5589 (mmp) REVERT: E 551 MET cc_start: 0.5454 (mmp) cc_final: 0.5241 (mmp) REVERT: E 636 GLU cc_start: 0.7533 (pt0) cc_final: 0.6777 (pp20) REVERT: E 637 PHE cc_start: 0.6057 (m-10) cc_final: 0.5838 (m-10) REVERT: F 186 GLU cc_start: 0.6636 (mp0) cc_final: 0.5575 (mt-10) REVERT: F 200 ASN cc_start: 0.6386 (m-40) cc_final: 0.6152 (m-40) REVERT: F 314 THR cc_start: 0.7187 (t) cc_final: 0.6324 (m) REVERT: F 616 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7437 (mmtt) outliers start: 110 outliers final: 71 residues processed: 630 average time/residue: 0.1792 time to fit residues: 182.3682 Evaluate side-chains 553 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 480 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 ILE 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 237 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 646 LEU 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 262 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 370 ILE 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 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 365 ILE 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 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 D residue 854 VAL Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 299 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 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 742 LEU Chi-restraints excluded: chain E residue 760 VAL 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 632 ILE Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 96 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 chunk 222 optimal weight: 0.0370 chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN B 692 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS C 778 GLN D 806 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 GLN F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104923 restraints weight = 70068.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.107398 restraints weight = 38791.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108987 restraints weight = 25436.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110058 restraints weight = 19101.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110575 restraints weight = 15796.130| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.8107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29005 Z= 0.140 Angle : 0.731 20.789 39185 Z= 0.356 Chirality : 0.045 0.211 4436 Planarity : 0.005 0.059 5114 Dihedral : 8.091 154.616 4064 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.96 % Allowed : 20.15 % Favored : 76.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3532 helix: 0.43 (0.12), residues: 1961 sheet: -1.90 (0.25), residues: 394 loop : -1.55 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 258 TYR 0.026 0.002 TYR F 322 PHE 0.021 0.002 PHE D 709 TRP 0.039 0.002 TRP C 462 HIS 0.022 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (28988) covalent geometry : angle 0.73088 / 0.36 (39185) hydrogen bonds : bond 0.04546 / 3.05 ( 1422) hydrogen bonds : angle 5.24062 / 3.69 ( 4203) Misc. bond : bond 0.00482 / 0.31 ( 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 611 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 523 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.7794 (p) cc_final: 0.7535 (p) REVERT: A 254 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5847 (pm20) REVERT: A 622 MET cc_start: 0.7771 (ppp) cc_final: 0.7426 (ppp) REVERT: A 808 TYR cc_start: 0.5852 (t80) cc_final: 0.5556 (t80) REVERT: A 817 LEU cc_start: 0.8645 (tp) cc_final: 0.8398 (tt) REVERT: B 387 PRO cc_start: 0.8937 (Cg_endo) cc_final: 0.8600 (Cg_exo) REVERT: B 585 ARG cc_start: 0.6745 (mtt-85) cc_final: 0.5663 (mtm-85) REVERT: B 601 PHE cc_start: 0.7567 (m-80) cc_final: 0.7347 (m-80) REVERT: B 690 LEU cc_start: 0.8356 (mt) cc_final: 0.8124 (mt) REVERT: B 715 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8090 (tt) REVERT: C 293 MET cc_start: 0.7646 (mmm) cc_final: 0.6941 (mmm) REVERT: C 298 MET cc_start: 0.8147 (mpp) cc_final: 0.7803 (mpp) REVERT: C 535 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 561 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7534 (tmm-80) REVERT: C 834 LEU cc_start: 0.8710 (pp) cc_final: 0.8467 (mp) REVERT: D 257 GLU cc_start: 0.6389 (tm-30) cc_final: 0.6109 (tm-30) REVERT: D 281 HIS cc_start: 0.5151 (OUTLIER) cc_final: 0.4741 (p-80) REVERT: D 368 PRO cc_start: 0.7564 (Cg_exo) cc_final: 0.7248 (Cg_endo) REVERT: D 396 GLU cc_start: 0.5473 (tp30) cc_final: 0.5097 (tp30) REVERT: D 716 MET cc_start: 0.7285 (ptp) cc_final: 0.7084 (ptm) REVERT: D 797 ASP cc_start: 0.7663 (t0) cc_final: 0.7423 (t0) REVERT: E 242 MET cc_start: 0.5588 (mmp) cc_final: 0.5346 (mmp) REVERT: E 283 MET cc_start: 0.2785 (OUTLIER) cc_final: 0.1486 (mtm) REVERT: E 310 CYS cc_start: 0.5599 (m) cc_final: 0.5264 (m) REVERT: E 636 GLU cc_start: 0.7489 (pt0) cc_final: 0.6673 (pp20) REVERT: F 186 GLU cc_start: 0.6819 (mp0) cc_final: 0.5929 (mt-10) REVERT: F 200 ASN cc_start: 0.6227 (m-40) cc_final: 0.6018 (m-40) REVERT: F 325 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8658 (mmtm) REVERT: F 616 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7429 (mmtm) REVERT: F 846 LEU cc_start: 0.7117 (tt) cc_final: 0.6840 (tp) outliers start: 88 outliers final: 57 residues processed: 579 average time/residue: 0.1842 time to fit residues: 175.0377 Evaluate side-chains 532 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 470 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 274 ILE 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 165 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL 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 536 ILE Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 761 VAL 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 282 THR Chi-restraints excluded: chain D residue 609 VAL 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 774 ILE Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 299 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 742 LEU Chi-restraints excluded: chain E residue 760 VAL 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 577 VAL Chi-restraints excluded: chain F residue 607 THR 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: 0.9980 chunk 33 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 692 GLN B 174 GLN B 736 HIS ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN E 824 GLN E 831 GLN E 849 ASN F 159 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101473 restraints weight = 70444.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103796 restraints weight = 40128.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105300 restraints weight = 26823.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.106244 restraints weight = 20420.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106757 restraints weight = 17192.867| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 1.0080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29005 Z= 0.218 Angle : 0.856 17.934 39185 Z= 0.427 Chirality : 0.050 0.314 4436 Planarity : 0.006 0.128 5114 Dihedral : 8.330 153.307 4064 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.29 % Allowed : 20.85 % Favored : 75.86 % 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: -1.01 (0.14), residues: 3532 helix: 0.14 (0.11), residues: 1979 sheet: -1.83 (0.24), residues: 388 loop : -1.49 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 845 TYR 0.025 0.002 TYR D 322 PHE 0.053 0.003 PHE D 333 TRP 0.038 0.002 TRP C 462 HIS 0.029 0.002 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (28988) covalent geometry : angle 0.85649 / 0.43 (39185) hydrogen bonds : bond 0.05215 / 3.52 ( 1422) hydrogen bonds : angle 5.46774 / 3.84 ( 4203) Misc. bond : bond 0.00333 / 0.23 ( 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 690 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 592 time to evaluate : 1.127 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: A 169 THR cc_start: 0.8319 (p) cc_final: 0.8049 (p) REVERT: A 533 ASP cc_start: 0.7147 (p0) cc_final: 0.6724 (t0) REVERT: A 551 MET cc_start: 0.6890 (tpp) cc_final: 0.6660 (tpp) REVERT: A 562 MET cc_start: 0.6813 (tpp) cc_final: 0.6431 (tpt) REVERT: A 696 ASP cc_start: 0.7368 (m-30) cc_final: 0.6928 (m-30) REVERT: A 745 VAL cc_start: 0.8486 (t) cc_final: 0.8208 (p) REVERT: A 750 ARG cc_start: 0.6743 (mtt180) cc_final: 0.6525 (mtt180) REVERT: C 293 MET cc_start: 0.8023 (mmm) cc_final: 0.6992 (mmm) REVERT: C 298 MET cc_start: 0.8444 (mpp) cc_final: 0.7992 (mpp) REVERT: C 317 ASP cc_start: 0.7651 (m-30) cc_final: 0.7369 (t0) REVERT: C 318 GLU cc_start: 0.7740 (mp0) cc_final: 0.7509 (mp0) REVERT: C 535 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7307 (mm-30) REVERT: D 257 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6508 (tm-30) REVERT: D 264 ASN cc_start: 0.8003 (m-40) cc_final: 0.7793 (m-40) REVERT: D 634 MET cc_start: 0.8631 (ttm) cc_final: 0.8373 (ttm) REVERT: D 637 PHE cc_start: 0.8280 (m-80) cc_final: 0.7986 (m-10) REVERT: D 644 SER cc_start: 0.7947 (m) cc_final: 0.7676 (p) REVERT: D 669 ARG cc_start: 0.8052 (mmp80) cc_final: 0.7706 (mmm-85) REVERT: D 675 LEU cc_start: 0.8748 (tp) cc_final: 0.7919 (tp) REVERT: D 676 LEU cc_start: 0.8505 (tt) cc_final: 0.7397 (tt) REVERT: D 729 PHE cc_start: 0.7114 (t80) cc_final: 0.6904 (t80) REVERT: E 186 GLU cc_start: 0.6459 (mp0) cc_final: 0.6216 (mp0) REVERT: E 322 TYR cc_start: 0.7478 (m-80) cc_final: 0.7144 (m-80) REVERT: E 396 GLU cc_start: 0.7615 (tt0) cc_final: 0.7118 (mp0) REVERT: E 406 ASP cc_start: 0.5421 (t0) cc_final: 0.4989 (m-30) REVERT: E 638 MET cc_start: 0.7829 (tpt) cc_final: 0.7449 (mmt) REVERT: E 646 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7286 (tt) REVERT: E 708 ASP cc_start: 0.6114 (t0) cc_final: 0.5372 (p0) REVERT: F 325 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8612 (mptt) REVERT: F 616 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7471 (mmtp) REVERT: F 639 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7190 (mp0) REVERT: F 698 ARG cc_start: 0.5884 (ttp80) cc_final: 0.5410 (ttp80) outliers start: 98 outliers final: 62 residues processed: 650 average time/residue: 0.1928 time to fit residues: 201.5406 Evaluate side-chains 539 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 476 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 624 ASP 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 238 LEU Chi-restraints excluded: chain B residue 330 GLU 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 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 C residue 166 ILE Chi-restraints excluded: chain C residue 201 ASN 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 415 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 754 ILE Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 381 ILE 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 E residue 204 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 299 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 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 744 VAL Chi-restraints excluded: chain E residue 749 PHE Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain E residue 760 VAL 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 559 LEU Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 644 SER Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 44 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 346 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 281 HIS C 334 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101302 restraints weight = 70801.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103650 restraints weight = 40022.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105226 restraints weight = 26612.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106101 restraints weight = 20139.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106838 restraints weight = 16924.889| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 1.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29005 Z= 0.169 Angle : 0.780 20.130 39185 Z= 0.384 Chirality : 0.048 0.341 4436 Planarity : 0.005 0.084 5114 Dihedral : 8.121 152.301 4064 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.99 % Allowed : 23.40 % Favored : 73.61 % 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: -0.77 (0.14), residues: 3532 helix: 0.33 (0.12), residues: 1981 sheet: -1.66 (0.25), residues: 390 loop : -1.40 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 384 TYR 0.022 0.002 TYR A 783 PHE 0.029 0.002 PHE E 749 TRP 0.054 0.002 TRP C 462 HIS 0.020 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (28988) covalent geometry : angle 0.77953 / 0.38 (39185) hydrogen bonds : bond 0.04671 / 3.14 ( 1422) hydrogen bonds : angle 5.30126 / 3.72 ( 4203) Misc. bond : bond 0.00800 / 0.51 ( 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 594 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 505 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.8413 (p) cc_final: 0.8137 (p) REVERT: A 254 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: A 264 ASN cc_start: 0.8734 (m-40) cc_final: 0.7906 (t0) REVERT: A 533 ASP cc_start: 0.7274 (p0) cc_final: 0.6979 (t0) REVERT: A 629 MET cc_start: 0.6612 (ttm) cc_final: 0.6349 (ttm) REVERT: A 696 ASP cc_start: 0.7773 (m-30) cc_final: 0.7387 (m-30) REVERT: A 745 VAL cc_start: 0.8408 (t) cc_final: 0.8132 (p) REVERT: B 535 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 737 MET cc_start: 0.7991 (mmm) cc_final: 0.7751 (tpp) REVERT: C 318 GLU cc_start: 0.7743 (mp0) cc_final: 0.7493 (mp0) REVERT: C 535 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7279 (mm-30) REVERT: D 257 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6501 (tm-30) REVERT: D 562 MET cc_start: 0.8484 (tpp) cc_final: 0.8184 (tpp) REVERT: D 634 MET cc_start: 0.8719 (ttm) cc_final: 0.8350 (ttm) REVERT: D 676 LEU cc_start: 0.8551 (tt) cc_final: 0.7564 (tt) REVERT: D 677 ASP cc_start: 0.8237 (t0) cc_final: 0.7858 (t0) REVERT: E 322 TYR cc_start: 0.7461 (m-80) cc_final: 0.7082 (m-80) REVERT: E 396 GLU cc_start: 0.7682 (tt0) cc_final: 0.7245 (mp0) REVERT: E 406 ASP cc_start: 0.5892 (t0) cc_final: 0.5568 (m-30) REVERT: E 638 MET cc_start: 0.8091 (tpt) cc_final: 0.7791 (mmt) REVERT: E 646 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7664 (tt) REVERT: E 686 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7470 (t) REVERT: E 708 ASP cc_start: 0.6853 (t0) cc_final: 0.5661 (p0) REVERT: E 809 ASP cc_start: 0.7860 (t0) cc_final: 0.7650 (t0) REVERT: F 325 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8574 (mmtm) REVERT: F 616 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7357 (mmtp) REVERT: F 639 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7142 (mp0) REVERT: F 698 ARG cc_start: 0.5852 (ttp80) cc_final: 0.5477 (ttp80) outliers start: 89 outliers final: 50 residues processed: 557 average time/residue: 0.1828 time to fit residues: 167.0286 Evaluate side-chains 499 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 445 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 624 ASP 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 238 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 742 LEU 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 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 712 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 266 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 686 VAL Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain F residue 198 THR 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 607 THR Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 287 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 129 optimal weight: 0.0170 chunk 109 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN ** B 297 ASN ** 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 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101663 restraints weight = 70691.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104009 restraints weight = 40111.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105547 restraints weight = 26832.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106407 restraints weight = 20433.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.107079 restraints weight = 17315.891| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 1.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29005 Z= 0.143 Angle : 0.772 18.437 39185 Z= 0.375 Chirality : 0.047 0.284 4436 Planarity : 0.005 0.059 5114 Dihedral : 8.023 150.987 4064 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.35 % Allowed : 24.48 % Favored : 73.17 % 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: -0.65 (0.14), residues: 3532 helix: 0.45 (0.12), residues: 1975 sheet: -1.61 (0.24), residues: 396 loop : -1.38 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 815 TYR 0.027 0.001 TYR F 661 PHE 0.035 0.002 PHE B 276 TRP 0.037 0.002 TRP C 462 HIS 0.017 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (28988) covalent geometry : angle 0.77197 / 0.37 (39185) hydrogen bonds : bond 0.04478 / 3.03 ( 1422) hydrogen bonds : angle 5.25659 / 3.68 ( 4203) Misc. bond : bond 0.00363 / 0.25 ( 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 562 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 492 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.8355 (p) cc_final: 0.8046 (p) REVERT: A 264 ASN cc_start: 0.8745 (m-40) cc_final: 0.7975 (t0) REVERT: A 320 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7227 (ttm170) REVERT: A 533 ASP cc_start: 0.7398 (p0) cc_final: 0.7188 (t0) REVERT: A 629 MET cc_start: 0.6627 (ttm) cc_final: 0.6421 (ttm) REVERT: A 696 ASP cc_start: 0.7813 (m-30) cc_final: 0.7360 (t0) REVERT: C 535 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 562 MET cc_start: 0.8240 (tpp) cc_final: 0.7725 (tpp) REVERT: D 257 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6550 (tm-30) REVERT: D 272 ASN cc_start: 0.5661 (m-40) cc_final: 0.5292 (p0) REVERT: D 562 MET cc_start: 0.8467 (tpp) cc_final: 0.8190 (tpp) REVERT: D 634 MET cc_start: 0.8576 (ttm) cc_final: 0.8308 (ttm) REVERT: D 676 LEU cc_start: 0.8379 (tt) cc_final: 0.7192 (tt) REVERT: D 691 LEU cc_start: 0.8423 (tt) cc_final: 0.8167 (tp) REVERT: E 322 TYR cc_start: 0.7449 (m-80) cc_final: 0.7095 (m-80) REVERT: E 396 GLU cc_start: 0.7647 (tt0) cc_final: 0.7265 (mp0) REVERT: E 406 ASP cc_start: 0.5934 (t0) cc_final: 0.5630 (m-30) REVERT: E 638 MET cc_start: 0.8077 (tpt) cc_final: 0.7762 (mmt) REVERT: E 646 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7684 (tp) REVERT: E 708 ASP cc_start: 0.6758 (t0) cc_final: 0.5753 (p0) REVERT: E 809 ASP cc_start: 0.7703 (t0) cc_final: 0.6706 (m-30) REVERT: E 826 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7114 (mm-30) REVERT: F 200 ASN cc_start: 0.7053 (m-40) cc_final: 0.6651 (t0) REVERT: F 616 LYS cc_start: 0.7605 (mmtm) cc_final: 0.7367 (mmtp) REVERT: F 698 ARG cc_start: 0.5874 (ttp80) cc_final: 0.5584 (ttp80) outliers start: 70 outliers final: 52 residues processed: 533 average time/residue: 0.1578 time to fit residues: 140.0481 Evaluate side-chains 500 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 447 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 624 ASP 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 238 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 742 LEU 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 662 LEU Chi-restraints excluded: chain C residue 800 LEU 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 280 LEU Chi-restraints excluded: chain D residue 310 CYS 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 176 LYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 266 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 683 HIS Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 749 PHE Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL 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 607 THR 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: 7.9990 chunk 258 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 353 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 221 GLN A 225 ASN A 692 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 736 HIS ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** 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 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN F 159 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097013 restraints weight = 71149.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099237 restraints weight = 41145.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100723 restraints weight = 27918.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101674 restraints weight = 21454.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102156 restraints weight = 18057.361| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 1.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29005 Z= 0.220 Angle : 0.864 17.843 39185 Z= 0.430 Chirality : 0.050 0.411 4436 Planarity : 0.006 0.172 5114 Dihedral : 8.367 148.856 4064 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.65 % Allowed : 24.48 % Favored : 72.87 % 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: -0.97 (0.14), residues: 3532 helix: 0.17 (0.12), residues: 1982 sheet: -1.71 (0.23), residues: 394 loop : -1.49 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 852 TYR 0.022 0.002 TYR B 164 PHE 0.034 0.003 PHE B 621 TRP 0.043 0.003 TRP C 462 HIS 0.024 0.002 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (28988) covalent geometry : angle 0.86394 / 0.43 (39185) hydrogen bonds : bond 0.05242 / 3.53 ( 1422) hydrogen bonds : angle 5.53932 / 3.90 ( 4203) Misc. bond : bond 0.00333 / 0.23 ( 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 566 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: A 320 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7830 (ttm170) REVERT: A 551 MET cc_start: 0.6574 (tpp) cc_final: 0.6211 (tpp) REVERT: A 629 MET cc_start: 0.7412 (ttm) cc_final: 0.7191 (ttm) REVERT: A 634 MET cc_start: 0.8265 (mmm) cc_final: 0.8039 (mmm) REVERT: A 696 ASP cc_start: 0.7853 (m-30) cc_final: 0.7570 (m-30) REVERT: A 783 TYR cc_start: 0.6574 (m-10) cc_final: 0.6173 (m-80) REVERT: B 812 TYR cc_start: 0.6919 (m-80) cc_final: 0.6719 (m-80) REVERT: C 242 MET cc_start: 0.8132 (ttt) cc_final: 0.7748 (tpp) REVERT: C 562 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7581 (tpp) REVERT: C 780 LYS cc_start: 0.8657 (mttp) cc_final: 0.8334 (mmtm) REVERT: C 806 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8329 (t0) REVERT: D 240 LEU cc_start: 0.7811 (pp) cc_final: 0.7520 (pp) REVERT: D 257 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6887 (tm-30) REVERT: D 272 ASN cc_start: 0.6487 (m-40) cc_final: 0.5697 (p0) REVERT: D 562 MET cc_start: 0.8665 (tpp) cc_final: 0.8380 (tpp) REVERT: D 675 LEU cc_start: 0.9240 (tp) cc_final: 0.8943 (tp) REVERT: D 677 ASP cc_start: 0.8303 (t0) cc_final: 0.8009 (t0) REVERT: E 322 TYR cc_start: 0.7483 (m-80) cc_final: 0.7112 (m-80) REVERT: E 395 ASP cc_start: 0.6459 (t0) cc_final: 0.5911 (t0) REVERT: E 396 GLU cc_start: 0.7824 (tt0) cc_final: 0.7313 (mp0) REVERT: E 406 ASP cc_start: 0.6392 (t0) cc_final: 0.6069 (m-30) REVERT: E 707 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6915 (m) REVERT: E 826 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7512 (mm-30) REVERT: F 698 ARG cc_start: 0.6071 (ttp80) cc_final: 0.5656 (ttp80) outliers start: 79 outliers final: 49 residues processed: 539 average time/residue: 0.1781 time to fit residues: 158.0682 Evaluate side-chains 484 residues out of total 2994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 431 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 624 ASP 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 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 713 VAL 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 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 806 ASN 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 280 LEU 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 D residue 803 LEU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 266 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 683 HIS Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain E residue 760 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 350 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 225 ASN A 692 GLN A 822 GLN B 159 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 HIS ** B 849 ASN ** 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 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096562 restraints weight = 71447.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098771 restraints weight = 41153.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100260 restraints weight = 27816.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101117 restraints weight = 21247.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101804 restraints weight = 18060.925| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 1.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.274 29005 Z= 0.288 Angle : 1.024 59.196 39185 Z= 0.542 Chirality : 0.052 0.723 4436 Planarity : 0.007 0.178 5114 Dihedral : 8.372 148.766 4064 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 1.98 % Allowed : 26.12 % Favored : 71.89 % Cbeta Deviations : 0.09 % 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: -0.99 (0.14), residues: 3532 helix: 0.14 (0.12), residues: 1978 sheet: -1.72 (0.23), residues: 394 loop : -1.49 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 756 TYR 0.028 0.002 TYR B 164 PHE 0.036 0.003 PHE A 749 TRP 0.047 0.005 TRP D 543 HIS 0.281 0.003 HIS B 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.29 (28988) covalent geometry : angle 1.02350 / 0.54 (39185) hydrogen bonds : bond 0.05304 / 3.59 ( 1422) hydrogen bonds : angle 5.56732 / 3.92 ( 4203) Misc. bond : bond 0.00294 / 0.20 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5765.89 seconds wall clock time: 100 minutes 16.62 seconds (6016.62 seconds total)