Starting phenix.real_space_refine on Sun Aug 24 14:51:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5d_24186/08_2025/7n5d_24186.map" } resolution = 2.8 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13516 2.51 5 N 3419 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.26 Number of scatterers: 20593 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3574 8.00 N 3419 7.00 C 13516 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=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 872.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 9 sheets defined 64.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.855A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 259 through 283 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'B' and resid 187 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 265 through 285 Processing helix chain 'C' and resid 295 through 329 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 331 No H-bonds generated for 'chain 'C' and resid 330 through 331' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.519A pdb=" N GLN C 350 " --> pdb=" O HIS C 346 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 524 Processing helix chain 'C' and resid 526 through 552 Processing helix chain 'C' and resid 556 through 590 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 661 through 678 Processing helix chain 'C' and resid 714 through 737 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 235 through 242 Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 295 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.541A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 524 Processing helix chain 'D' and resid 526 through 552 Processing helix chain 'D' and resid 556 through 590 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 714 through 737 Processing helix chain 'E' and resid 187 through 203 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 265 through 285 Processing helix chain 'E' and resid 295 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.661A pdb=" N GLN E 350 " --> pdb=" O HIS E 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 524 Processing helix chain 'E' and resid 526 through 552 Processing helix chain 'E' and resid 556 through 590 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'E' and resid 661 through 678 Processing helix chain 'E' and resid 714 through 736 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.722A pdb=" N GLY F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 Processing helix chain 'F' and resid 265 through 285 Processing helix chain 'F' and resid 295 through 329 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 331 No H-bonds generated for 'chain 'F' and resid 330 through 331' Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 352 Processing helix chain 'F' and resid 508 through 524 Processing helix chain 'F' and resid 526 through 552 Processing helix chain 'F' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 661 through 678 Processing helix chain 'F' and resid 714 through 737 Processing helix chain 'G' and resid 187 through 203 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 235 through 242 Processing helix chain 'G' and resid 265 through 285 Processing helix chain 'G' and resid 295 through 329 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 331 No H-bonds generated for 'chain 'G' and resid 330 through 331' Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 508 through 524 Processing helix chain 'G' and resid 526 through 552 Processing helix chain 'G' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 661 through 678 Processing helix chain 'G' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 626 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 626 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 626 " --> pdb=" O ASN D 641 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 626 " --> pdb=" O ASN E 641 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS E 626 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS F 626 " --> pdb=" O ASN G 641 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS G 626 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 750 removed outlier: 6.485A pdb=" N GLN A 745 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG B 750 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 747 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE G 749 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.484A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.416A pdb=" N LYS C 699 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 694 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 701 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 707 " --> pdb=" O GLN C 686 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 686 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.507A pdb=" N LYS D 699 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE D 694 " --> pdb=" O LYS D 699 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 701 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.465A pdb=" N LYS E 699 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 694 " --> pdb=" O LYS E 699 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 701 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.506A pdb=" N LYS F 699 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE F 694 " --> pdb=" O LYS F 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS F 701 " --> pdb=" O LYS F 692 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN F 707 " --> pdb=" O GLN F 686 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN F 686 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.330A pdb=" N LYS G 699 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE G 694 " --> pdb=" O LYS G 699 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS G 701 " --> pdb=" O LYS G 692 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 707 " --> pdb=" O GLN G 686 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN G 686 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4437 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: 3.85 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3829 1.31 - 1.44: 5375 1.44 - 1.56: 11510 1.56 - 1.69: 113 1.69 - 1.82: 147 Bond restraints: 20974 Sorted by residual: bond pdb=" CB ILE E 285 " pdb=" CG1 ILE E 285 " ideal model delta sigma weight residual 1.530 1.672 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CB ILE F 285 " pdb=" CG1 ILE F 285 " ideal model delta sigma weight residual 1.530 1.671 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" CB ILE G 285 " pdb=" CG1 ILE G 285 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 ... (remaining 20969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 22909 1.77 - 3.54: 4432 3.54 - 5.31: 876 5.31 - 7.07: 184 7.07 - 8.84: 23 Bond angle restraints: 28424 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 28419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 12108 17.71 - 35.42: 257 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 12457 sinusoidal: 4779 harmonic: 7678 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2784 0.110 - 0.220: 601 0.220 - 0.330: 46 0.330 - 0.440: 9 0.440 - 0.550: 12 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.14 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 3449 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 7757 2.88 - 3.39: 21201 3.39 - 3.89: 34646 3.89 - 4.40: 39809 4.40 - 4.90: 62906 Nonbonded interactions: 166319 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 3.120 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 3.120 ... (remaining 166314 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 186 through 203 or resid 222 through 242 or resid 264 thro \ ugh 354 or resid 507 through 801)) selection = (chain 'B' and (resid 186 through 285 or resid 294 through 801)) selection = (chain 'C' and (resid 186 through 285 or resid 294 through 801)) selection = (chain 'D' and (resid 186 through 285 or resid 294 through 801)) selection = (chain 'E' and (resid 186 through 285 or resid 294 through 801)) selection = (chain 'F' and (resid 186 through 285 or resid 294 through 801)) selection = (chain 'G' and (resid 186 through 285 or resid 294 through 801)) } 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 individual isotropic 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.023 0.142 20974 Z= 1.204 Angle : 1.521 8.842 28424 Z= 1.044 Chirality : 0.093 0.550 3452 Planarity : 0.008 0.043 3469 Dihedral : 9.909 88.544 7391 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.83 (0.15), residues: 2540 helix: 1.53 (0.11), residues: 1580 sheet: 0.56 (0.31), residues: 290 loop : 1.05 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 334 TYR 0.044 0.008 TYR E 675 PHE 0.059 0.005 PHE A 335 TRP 0.036 0.008 TRP E 683 HIS 0.010 0.002 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.02258 (20974) covalent geometry : angle 1.52089 (28424) hydrogen bonds : bond 0.13890 ( 1505) hydrogen bonds : angle 5.98927 ( 4437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 794 time to evaluate : 0.827 Fit side-chains REVERT: A 311 ILE cc_start: 0.8728 (mt) cc_final: 0.8502 (mm) REVERT: A 325 ILE cc_start: 0.8581 (mt) cc_final: 0.8294 (mt) REVERT: A 525 ASN cc_start: 0.7725 (t0) cc_final: 0.7345 (t0) REVERT: B 300 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7184 (mp0) REVERT: B 526 LYS cc_start: 0.8486 (mttt) cc_final: 0.7916 (mtpp) REVERT: C 304 TRP cc_start: 0.8104 (m100) cc_final: 0.7693 (m100) REVERT: C 525 ASN cc_start: 0.7029 (t0) cc_final: 0.5993 (t0) REVERT: C 526 LYS cc_start: 0.7602 (mttt) cc_final: 0.7398 (mmmm) REVERT: C 595 ASP cc_start: 0.7585 (m-30) cc_final: 0.7253 (m-30) REVERT: D 314 PHE cc_start: 0.8224 (t80) cc_final: 0.7703 (t80) REVERT: D 329 SER cc_start: 0.8520 (m) cc_final: 0.7877 (p) REVERT: D 526 LYS cc_start: 0.8635 (mttt) cc_final: 0.8422 (mmtm) REVERT: D 621 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7421 (mtmt) REVERT: D 625 GLU cc_start: 0.7377 (tt0) cc_final: 0.6938 (tt0) REVERT: F 671 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: F 717 GLU cc_start: 0.8625 (tp30) cc_final: 0.8381 (mm-30) REVERT: F 735 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 282 VAL cc_start: 0.7420 (m) cc_final: 0.7153 (p) REVERT: G 526 LYS cc_start: 0.8236 (mttt) cc_final: 0.8028 (mptt) REVERT: G 748 SER cc_start: 0.8856 (t) cc_final: 0.8640 (p) outliers start: 0 outliers final: 6 residues processed: 794 average time/residue: 0.6411 time to fit residues: 574.1298 Evaluate side-chains 646 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 640 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain G residue 311 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.0170 chunk 258 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 515 GLN A 576 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 576 ASN C 648 GLN D 291 GLN D 525 ASN D 576 ASN D 687 HIS D 713 GLN E 533 ASN E 648 GLN F 345 HIS F 525 ASN F 648 GLN G 533 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107354 restraints weight = 33116.925| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.90 r_work: 0.3319 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20974 Z= 0.153 Angle : 0.586 9.184 28424 Z= 0.308 Chirality : 0.043 0.284 3452 Planarity : 0.003 0.043 3469 Dihedral : 7.028 59.049 2793 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.85 % Allowed : 13.44 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.84 (0.16), residues: 2540 helix: 2.59 (0.12), residues: 1612 sheet: 0.55 (0.29), residues: 299 loop : 0.77 (0.27), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 296 TYR 0.010 0.001 TYR A 259 PHE 0.021 0.002 PHE D 301 TRP 0.017 0.002 TRP B 273 HIS 0.007 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00322 (20974) covalent geometry : angle 0.58596 (28424) hydrogen bonds : bond 0.05627 ( 1505) hydrogen bonds : angle 4.25036 ( 4437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 686 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 302 VAL cc_start: 0.8693 (t) cc_final: 0.8473 (m) REVERT: A 330 PHE cc_start: 0.7773 (t80) cc_final: 0.7514 (t80) REVERT: A 576 ASN cc_start: 0.7823 (t0) cc_final: 0.7202 (t0) REVERT: A 647 ASP cc_start: 0.8140 (m-30) cc_final: 0.7925 (m-30) REVERT: A 723 SER cc_start: 0.8521 (t) cc_final: 0.8234 (m) REVERT: A 737 ASP cc_start: 0.8225 (t0) cc_final: 0.7920 (t0) REVERT: B 324 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7924 (mmtt) REVERT: B 328 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8536 (t) REVERT: B 568 VAL cc_start: 0.8519 (p) cc_final: 0.8303 (p) REVERT: B 583 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 686 GLN cc_start: 0.8358 (mp-120) cc_final: 0.7852 (mp10) REVERT: C 304 TRP cc_start: 0.7780 (m100) cc_final: 0.7576 (m100) REVERT: C 560 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8182 (tt) REVERT: C 579 LYS cc_start: 0.8862 (tmmm) cc_final: 0.8655 (tttp) REVERT: C 595 ASP cc_start: 0.8028 (m-30) cc_final: 0.7825 (m-30) REVERT: D 307 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8474 (m) REVERT: D 314 PHE cc_start: 0.8064 (t80) cc_final: 0.7788 (t80) REVERT: D 737 ASP cc_start: 0.8256 (t0) cc_final: 0.7949 (t0) REVERT: D 739 LYS cc_start: 0.8624 (mttp) cc_final: 0.8370 (mttp) REVERT: E 530 LYS cc_start: 0.8831 (mttt) cc_final: 0.8613 (mtpp) REVERT: E 624 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8509 (mmtp) REVERT: F 548 TRP cc_start: 0.8186 (t60) cc_final: 0.7527 (t60) REVERT: F 572 PHE cc_start: 0.7968 (t80) cc_final: 0.7754 (t80) REVERT: F 671 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8165 (mmm-85) REVERT: F 673 LYS cc_start: 0.8627 (tttt) cc_final: 0.8259 (tttp) REVERT: F 735 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7824 (mt-10) REVERT: G 324 LYS cc_start: 0.8403 (mttm) cc_final: 0.8109 (mttm) REVERT: G 530 LYS cc_start: 0.8625 (mttt) cc_final: 0.8380 (mttp) REVERT: G 561 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (m) REVERT: G 715 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: G 737 ASP cc_start: 0.8050 (t0) cc_final: 0.7823 (t0) REVERT: G 748 SER cc_start: 0.8942 (t) cc_final: 0.8656 (p) outliers start: 83 outliers final: 31 residues processed: 712 average time/residue: 0.5649 time to fit residues: 457.2393 Evaluate side-chains 682 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 646 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain G residue 561 VAL Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 145 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 218 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.0050 chunk 170 optimal weight: 0.0060 chunk 234 optimal weight: 5.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 533 ASN A 605 ASN A 686 GLN B 576 ASN B 686 GLN B 696 ASN C 648 GLN C 713 GLN D 291 GLN D 648 GLN D 719 ASN E 648 GLN E 698 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN G 525 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107443 restraints weight = 33023.935| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.95 r_work: 0.3322 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20974 Z= 0.129 Angle : 0.525 8.015 28424 Z= 0.272 Chirality : 0.041 0.256 3452 Planarity : 0.003 0.039 3469 Dihedral : 6.726 59.963 2785 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.94 % Allowed : 17.43 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.84 (0.17), residues: 2540 helix: 2.75 (0.12), residues: 1613 sheet: 0.20 (0.29), residues: 311 loop : 0.48 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 720 TYR 0.009 0.001 TYR E 740 PHE 0.025 0.001 PHE G 301 TRP 0.023 0.001 TRP C 273 HIS 0.005 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00274 (20974) covalent geometry : angle 0.52453 (28424) hydrogen bonds : bond 0.04645 ( 1505) hydrogen bonds : angle 4.01151 ( 4437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 653 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 302 VAL cc_start: 0.8580 (t) cc_final: 0.8368 (m) REVERT: A 311 ILE cc_start: 0.8840 (tp) cc_final: 0.8622 (tp) REVERT: A 526 LYS cc_start: 0.8077 (mttt) cc_final: 0.7785 (ttmm) REVERT: A 576 ASN cc_start: 0.7939 (t0) cc_final: 0.7516 (t0) REVERT: A 647 ASP cc_start: 0.8160 (m-30) cc_final: 0.7915 (m-30) REVERT: A 671 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8715 (mmm-85) REVERT: A 717 GLU cc_start: 0.7801 (tp30) cc_final: 0.7492 (tp30) REVERT: A 723 SER cc_start: 0.8501 (t) cc_final: 0.8257 (m) REVERT: A 737 ASP cc_start: 0.8231 (t0) cc_final: 0.7760 (t0) REVERT: B 324 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8060 (mmtt) REVERT: B 583 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 686 GLN cc_start: 0.8370 (mp10) cc_final: 0.7913 (mp10) REVERT: C 304 TRP cc_start: 0.7767 (m100) cc_final: 0.7560 (m-90) REVERT: C 306 ILE cc_start: 0.8256 (mm) cc_final: 0.7977 (tp) REVERT: C 526 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7703 (mmtt) REVERT: D 282 VAL cc_start: 0.8012 (p) cc_final: 0.7765 (m) REVERT: D 314 PHE cc_start: 0.8063 (t80) cc_final: 0.7825 (t80) REVERT: D 526 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8140 (mmtm) REVERT: D 534 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8684 (mtpt) REVERT: D 579 LYS cc_start: 0.8825 (tmmm) cc_final: 0.8573 (tttm) REVERT: D 664 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7830 (tptm) REVERT: D 737 ASP cc_start: 0.8263 (t0) cc_final: 0.7913 (t0) REVERT: D 739 LYS cc_start: 0.8640 (mttp) cc_final: 0.8367 (mttp) REVERT: E 318 VAL cc_start: 0.9061 (t) cc_final: 0.8817 (p) REVERT: E 325 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8570 (pp) REVERT: E 530 LYS cc_start: 0.8711 (mttt) cc_final: 0.8504 (mtmm) REVERT: E 583 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8196 (mt-10) REVERT: E 624 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8574 (mmtp) REVERT: F 548 TRP cc_start: 0.8207 (t60) cc_final: 0.7596 (t60) REVERT: F 610 GLU cc_start: 0.8109 (tp30) cc_final: 0.7909 (tp30) REVERT: F 653 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: F 671 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8223 (mmm-85) REVERT: F 701 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8540 (mtmt) REVERT: F 735 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7813 (mt-10) REVERT: G 324 LYS cc_start: 0.8515 (mttm) cc_final: 0.8208 (mttm) REVERT: G 530 LYS cc_start: 0.8609 (mttt) cc_final: 0.8365 (mttp) REVERT: G 737 ASP cc_start: 0.8061 (t0) cc_final: 0.7808 (t0) REVERT: G 748 SER cc_start: 0.8924 (t) cc_final: 0.8643 (p) outliers start: 85 outliers final: 41 residues processed: 680 average time/residue: 0.5567 time to fit residues: 430.2583 Evaluate side-chains 682 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 636 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 678 GLN Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain F residue 739 LYS Chi-restraints excluded: chain G residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 214 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 166 optimal weight: 0.0000 chunk 124 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 566 GLN A 686 GLN ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN D 531 GLN D 576 ASN D 698 ASN E 531 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106724 restraints weight = 33033.618| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.94 r_work: 0.3319 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20974 Z= 0.133 Angle : 0.525 13.194 28424 Z= 0.266 Chirality : 0.041 0.312 3452 Planarity : 0.003 0.062 3469 Dihedral : 6.469 58.297 2781 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.89 % Allowed : 18.59 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.92 (0.17), residues: 2540 helix: 2.84 (0.12), residues: 1612 sheet: 0.37 (0.27), residues: 329 loop : 0.33 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 720 TYR 0.012 0.001 TYR F 740 PHE 0.022 0.001 PHE A 271 TRP 0.019 0.001 TRP A 316 HIS 0.004 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00297 (20974) covalent geometry : angle 0.52519 (28424) hydrogen bonds : bond 0.04394 ( 1505) hydrogen bonds : angle 3.91608 ( 4437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 636 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7011 (pmt170) cc_final: 0.6781 (pmt170) REVERT: A 300 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 311 ILE cc_start: 0.8840 (tp) cc_final: 0.8603 (OUTLIER) REVERT: A 526 LYS cc_start: 0.8238 (mttt) cc_final: 0.7947 (ttmm) REVERT: A 576 ASN cc_start: 0.7986 (t0) cc_final: 0.7587 (t0) REVERT: A 647 ASP cc_start: 0.8152 (m-30) cc_final: 0.7888 (m-30) REVERT: A 671 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: A 717 GLU cc_start: 0.7835 (tp30) cc_final: 0.7531 (tp30) REVERT: A 723 SER cc_start: 0.8471 (t) cc_final: 0.8203 (m) REVERT: A 737 ASP cc_start: 0.8184 (t0) cc_final: 0.7757 (t0) REVERT: B 583 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 686 GLN cc_start: 0.8403 (mp10) cc_final: 0.7877 (mp10) REVERT: C 670 ASP cc_start: 0.8104 (m-30) cc_final: 0.7893 (m-30) REVERT: D 314 PHE cc_start: 0.8024 (t80) cc_final: 0.7814 (t80) REVERT: D 526 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8042 (mmtm) REVERT: D 534 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8623 (mtpt) REVERT: D 579 LYS cc_start: 0.8808 (tmmm) cc_final: 0.8604 (ttpp) REVERT: D 624 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8494 (mmtm) REVERT: D 664 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7824 (tptm) REVERT: D 737 ASP cc_start: 0.8297 (t0) cc_final: 0.7891 (t0) REVERT: D 739 LYS cc_start: 0.8596 (mttp) cc_final: 0.8262 (mttp) REVERT: E 318 VAL cc_start: 0.9040 (t) cc_final: 0.8810 (p) REVERT: E 325 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8544 (pp) REVERT: E 530 LYS cc_start: 0.8670 (mttt) cc_final: 0.8416 (mtmm) REVERT: E 624 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8567 (mmtp) REVERT: F 548 TRP cc_start: 0.8200 (t60) cc_final: 0.7836 (t60) REVERT: F 610 GLU cc_start: 0.8041 (tp30) cc_final: 0.7814 (tp30) REVERT: F 653 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: F 671 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8314 (mmm-85) REVERT: F 701 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8527 (mtmt) REVERT: F 715 PHE cc_start: 0.8328 (t80) cc_final: 0.8072 (t80) REVERT: F 735 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7905 (mt-10) REVERT: G 324 LYS cc_start: 0.8561 (mttm) cc_final: 0.8346 (mttm) REVERT: G 530 LYS cc_start: 0.8586 (mttt) cc_final: 0.8235 (mttp) REVERT: G 534 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8846 (mttp) REVERT: G 545 ILE cc_start: 0.8759 (mp) cc_final: 0.8491 (mp) REVERT: G 715 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: G 737 ASP cc_start: 0.8060 (t0) cc_final: 0.7764 (t0) REVERT: G 748 SER cc_start: 0.8921 (t) cc_final: 0.8647 (p) outliers start: 84 outliers final: 50 residues processed: 663 average time/residue: 0.5480 time to fit residues: 412.2789 Evaluate side-chains 671 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 616 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 18 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 533 ASN A 686 GLN B 613 ASN C 648 GLN C 698 ASN D 531 GLN E 648 GLN E 688 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107964 restraints weight = 32457.127| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.01 r_work: 0.3291 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20974 Z= 0.187 Angle : 0.545 10.453 28424 Z= 0.280 Chirality : 0.043 0.374 3452 Planarity : 0.003 0.037 3469 Dihedral : 6.382 57.781 2781 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.40 % Allowed : 18.82 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.87 (0.17), residues: 2540 helix: 2.83 (0.12), residues: 1612 sheet: 0.22 (0.27), residues: 341 loop : 0.32 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 644 TYR 0.013 0.002 TYR F 740 PHE 0.024 0.002 PHE F 301 TRP 0.019 0.002 TRP A 316 HIS 0.007 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00444 (20974) covalent geometry : angle 0.54513 (28424) hydrogen bonds : bond 0.04649 ( 1505) hydrogen bonds : angle 3.95958 ( 4437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 629 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7018 (pmt170) cc_final: 0.6795 (pmt170) REVERT: A 300 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 311 ILE cc_start: 0.8896 (tp) cc_final: 0.8664 (tp) REVERT: A 323 LEU cc_start: 0.8516 (mt) cc_final: 0.8191 (tm) REVERT: A 576 ASN cc_start: 0.8028 (t0) cc_final: 0.7649 (t0) REVERT: A 647 ASP cc_start: 0.8181 (m-30) cc_final: 0.7897 (m-30) REVERT: A 723 SER cc_start: 0.8483 (t) cc_final: 0.8258 (m) REVERT: A 737 ASP cc_start: 0.8232 (t0) cc_final: 0.7790 (t0) REVERT: B 324 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7957 (mmtt) REVERT: B 583 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 629 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8205 (t80) REVERT: B 686 GLN cc_start: 0.8368 (mp10) cc_final: 0.7830 (mp10) REVERT: B 689 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8484 (ttp) REVERT: B 697 VAL cc_start: 0.7888 (m) cc_final: 0.7673 (t) REVERT: C 306 ILE cc_start: 0.8323 (mm) cc_final: 0.8014 (tp) REVERT: C 670 ASP cc_start: 0.8098 (m-30) cc_final: 0.7893 (m-30) REVERT: D 526 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mmtm) REVERT: D 534 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8631 (mtpt) REVERT: D 624 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8523 (mmtm) REVERT: D 737 ASP cc_start: 0.8287 (t0) cc_final: 0.7812 (t0) REVERT: D 739 LYS cc_start: 0.8576 (mttp) cc_final: 0.8169 (mttp) REVERT: E 318 VAL cc_start: 0.9057 (t) cc_final: 0.8833 (p) REVERT: E 325 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8537 (pp) REVERT: E 624 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8562 (mmtp) REVERT: F 548 TRP cc_start: 0.8234 (t60) cc_final: 0.7938 (t60) REVERT: F 610 GLU cc_start: 0.8086 (tp30) cc_final: 0.7855 (tp30) REVERT: F 653 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: F 671 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8247 (mmm160) REVERT: F 695 GLU cc_start: 0.8280 (tt0) cc_final: 0.8079 (tt0) REVERT: F 701 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8514 (mtmt) REVERT: F 715 PHE cc_start: 0.8389 (t80) cc_final: 0.8146 (t80) REVERT: F 735 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7897 (mt-10) REVERT: G 324 LYS cc_start: 0.8603 (mttm) cc_final: 0.8355 (mttm) REVERT: G 530 LYS cc_start: 0.8629 (mttt) cc_final: 0.8284 (mttp) REVERT: G 534 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8859 (mttp) REVERT: G 545 ILE cc_start: 0.8713 (mp) cc_final: 0.8442 (mp) REVERT: G 715 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: G 737 ASP cc_start: 0.8066 (t0) cc_final: 0.7731 (t0) REVERT: G 748 SER cc_start: 0.8907 (t) cc_final: 0.8641 (p) outliers start: 95 outliers final: 50 residues processed: 659 average time/residue: 0.4979 time to fit residues: 372.1398 Evaluate side-chains 686 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 629 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 126 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 252 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 686 GLN B 613 ASN C 576 ASN C 648 GLN D 531 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 613 ASN G 681 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109089 restraints weight = 32359.624| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.01 r_work: 0.3317 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20974 Z= 0.134 Angle : 0.521 9.487 28424 Z= 0.264 Chirality : 0.042 0.272 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.263 59.348 2781 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.22 % Allowed : 19.19 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.97 (0.17), residues: 2540 helix: 2.95 (0.12), residues: 1612 sheet: 0.21 (0.27), residues: 341 loop : 0.26 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 720 TYR 0.009 0.001 TYR F 740 PHE 0.021 0.001 PHE A 271 TRP 0.026 0.001 TRP A 316 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00303 (20974) covalent geometry : angle 0.52136 (28424) hydrogen bonds : bond 0.04265 ( 1505) hydrogen bonds : angle 3.88932 ( 4437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 628 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6996 (pmt170) cc_final: 0.6762 (pmt170) REVERT: A 300 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 311 ILE cc_start: 0.8865 (tp) cc_final: 0.8644 (tp) REVERT: A 323 LEU cc_start: 0.8498 (mt) cc_final: 0.8183 (tm) REVERT: A 526 LYS cc_start: 0.8196 (mttt) cc_final: 0.7921 (ttmm) REVERT: A 576 ASN cc_start: 0.8014 (t0) cc_final: 0.7645 (t0) REVERT: A 579 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8167 (ttpt) REVERT: A 647 ASP cc_start: 0.8153 (m-30) cc_final: 0.7863 (m-30) REVERT: A 717 GLU cc_start: 0.7616 (tp30) cc_final: 0.7276 (tp30) REVERT: A 723 SER cc_start: 0.8461 (t) cc_final: 0.8207 (m) REVERT: A 737 ASP cc_start: 0.8235 (t0) cc_final: 0.7781 (t0) REVERT: B 324 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8012 (mmtt) REVERT: B 583 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 629 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8187 (t80) REVERT: B 686 GLN cc_start: 0.8386 (mp10) cc_final: 0.8133 (mp10) REVERT: B 689 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (ttp) REVERT: B 697 VAL cc_start: 0.7897 (m) cc_final: 0.7682 (t) REVERT: C 300 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: C 670 ASP cc_start: 0.8112 (m-30) cc_final: 0.7830 (m-30) REVERT: C 689 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: D 526 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8054 (mmtm) REVERT: D 534 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8607 (mtpt) REVERT: D 548 TRP cc_start: 0.7622 (t60) cc_final: 0.7032 (t60) REVERT: D 624 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8505 (mmtm) REVERT: D 701 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8551 (mmtp) REVERT: D 723 SER cc_start: 0.8441 (t) cc_final: 0.8225 (p) REVERT: E 283 MET cc_start: 0.6632 (tpp) cc_final: 0.6092 (mpp) REVERT: E 318 VAL cc_start: 0.9052 (t) cc_final: 0.8831 (p) REVERT: E 325 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8533 (pp) REVERT: E 541 ILE cc_start: 0.8667 (mt) cc_final: 0.8453 (mp) REVERT: E 624 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8552 (mmtp) REVERT: E 739 LYS cc_start: 0.8783 (mttp) cc_final: 0.8467 (mttp) REVERT: F 548 TRP cc_start: 0.8214 (t60) cc_final: 0.7997 (t60) REVERT: F 610 GLU cc_start: 0.8057 (tp30) cc_final: 0.7794 (tp30) REVERT: F 653 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: F 671 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8238 (mmm160) REVERT: F 695 GLU cc_start: 0.8280 (tt0) cc_final: 0.8069 (tt0) REVERT: F 701 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8507 (mtmt) REVERT: F 715 PHE cc_start: 0.8327 (t80) cc_final: 0.8077 (t80) REVERT: F 735 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7885 (mt-10) REVERT: G 324 LYS cc_start: 0.8588 (mttm) cc_final: 0.8334 (mttm) REVERT: G 530 LYS cc_start: 0.8606 (mttt) cc_final: 0.8240 (mptp) REVERT: G 534 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8829 (mttp) REVERT: G 544 MET cc_start: 0.8078 (mmm) cc_final: 0.7827 (mmm) REVERT: G 545 ILE cc_start: 0.8687 (mp) cc_final: 0.8442 (mp) REVERT: G 737 ASP cc_start: 0.8054 (t0) cc_final: 0.7754 (t0) REVERT: G 748 SER cc_start: 0.8904 (t) cc_final: 0.8676 (p) outliers start: 91 outliers final: 47 residues processed: 662 average time/residue: 0.5291 time to fit residues: 397.7075 Evaluate side-chains 673 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 618 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 701 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 2 optimal weight: 9.9990 chunk 196 optimal weight: 0.0060 chunk 144 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 686 GLN B 613 ASN C 576 ASN C 648 GLN C 698 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106425 restraints weight = 33026.758| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.97 r_work: 0.3313 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20974 Z= 0.133 Angle : 0.527 8.915 28424 Z= 0.267 Chirality : 0.041 0.262 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.161 58.015 2781 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.08 % Allowed : 19.19 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.98 (0.17), residues: 2540 helix: 2.97 (0.12), residues: 1612 sheet: 0.16 (0.27), residues: 341 loop : 0.25 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 599 TYR 0.011 0.001 TYR D 740 PHE 0.029 0.001 PHE G 301 TRP 0.031 0.001 TRP A 316 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00302 (20974) covalent geometry : angle 0.52657 (28424) hydrogen bonds : bond 0.04174 ( 1505) hydrogen bonds : angle 3.86529 ( 4437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 619 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7025 (pmt170) cc_final: 0.6794 (pmt170) REVERT: A 300 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 311 ILE cc_start: 0.8855 (tp) cc_final: 0.8631 (tp) REVERT: A 323 LEU cc_start: 0.8479 (mt) cc_final: 0.8171 (tm) REVERT: A 526 LYS cc_start: 0.8290 (mttt) cc_final: 0.8058 (mmmm) REVERT: A 576 ASN cc_start: 0.8026 (t0) cc_final: 0.7675 (t0) REVERT: A 647 ASP cc_start: 0.8168 (m-30) cc_final: 0.7863 (m-30) REVERT: A 717 GLU cc_start: 0.7660 (tp30) cc_final: 0.7351 (tp30) REVERT: A 723 SER cc_start: 0.8457 (t) cc_final: 0.8196 (m) REVERT: A 737 ASP cc_start: 0.8189 (t0) cc_final: 0.7741 (t0) REVERT: B 324 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8087 (mmtt) REVERT: B 629 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8213 (t80) REVERT: B 686 GLN cc_start: 0.8389 (mp10) cc_final: 0.8134 (mp10) REVERT: B 689 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8487 (ttp) REVERT: C 670 ASP cc_start: 0.8094 (m-30) cc_final: 0.7797 (m-30) REVERT: C 689 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8500 (ttp) REVERT: C 735 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 526 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8071 (mmtm) REVERT: D 579 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8588 (ttpp) REVERT: D 624 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8493 (mmtm) REVERT: D 701 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8544 (mmtp) REVERT: E 283 MET cc_start: 0.6616 (tpp) cc_final: 0.6082 (mpp) REVERT: E 318 VAL cc_start: 0.9049 (t) cc_final: 0.8824 (p) REVERT: E 325 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8550 (pp) REVERT: E 541 ILE cc_start: 0.8674 (mt) cc_final: 0.8468 (mp) REVERT: E 579 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (tmtp) REVERT: E 624 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8560 (mmtp) REVERT: E 647 ASP cc_start: 0.7960 (m-30) cc_final: 0.7730 (m-30) REVERT: F 548 TRP cc_start: 0.8197 (t60) cc_final: 0.7996 (t60) REVERT: F 574 PHE cc_start: 0.6058 (m-10) cc_final: 0.5704 (m-10) REVERT: F 610 GLU cc_start: 0.8008 (tp30) cc_final: 0.7757 (tp30) REVERT: F 653 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: F 671 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8238 (mmm160) REVERT: F 695 GLU cc_start: 0.8297 (tt0) cc_final: 0.8085 (tt0) REVERT: F 701 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8490 (mtmt) REVERT: F 715 PHE cc_start: 0.8317 (t80) cc_final: 0.8079 (t80) REVERT: F 735 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7899 (mt-10) REVERT: G 530 LYS cc_start: 0.8575 (mttt) cc_final: 0.8209 (mptp) REVERT: G 531 GLN cc_start: 0.8225 (mt0) cc_final: 0.7866 (mt0) REVERT: G 534 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8823 (mttp) REVERT: G 673 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8581 (ttmm) REVERT: G 737 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7707 (t0) REVERT: G 748 SER cc_start: 0.8896 (t) cc_final: 0.8673 (p) outliers start: 88 outliers final: 55 residues processed: 650 average time/residue: 0.5649 time to fit residues: 415.7462 Evaluate side-chains 682 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 617 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 701 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 579 LYS Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 737 ASP Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 238 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106306 restraints weight = 33061.823| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.96 r_work: 0.3317 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20974 Z= 0.138 Angle : 0.547 9.639 28424 Z= 0.276 Chirality : 0.041 0.298 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.098 59.117 2781 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.76 % Allowed : 20.17 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 3.00 (0.17), residues: 2540 helix: 3.00 (0.12), residues: 1613 sheet: 0.12 (0.27), residues: 341 loop : 0.22 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.012 0.001 TYR D 740 PHE 0.024 0.001 PHE D 301 TRP 0.037 0.001 TRP A 316 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00313 (20974) covalent geometry : angle 0.54745 (28424) hydrogen bonds : bond 0.04161 ( 1505) hydrogen bonds : angle 3.87920 ( 4437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 620 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7027 (pmt170) cc_final: 0.6805 (pmt170) REVERT: A 300 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 311 ILE cc_start: 0.8876 (tp) cc_final: 0.8657 (tp) REVERT: A 323 LEU cc_start: 0.8478 (mt) cc_final: 0.8175 (tm) REVERT: A 526 LYS cc_start: 0.8256 (mttt) cc_final: 0.8034 (mmmm) REVERT: A 576 ASN cc_start: 0.8062 (t0) cc_final: 0.7715 (t0) REVERT: A 647 ASP cc_start: 0.8192 (m-30) cc_final: 0.7913 (m-30) REVERT: A 717 GLU cc_start: 0.7675 (tp30) cc_final: 0.7362 (tp30) REVERT: A 723 SER cc_start: 0.8457 (t) cc_final: 0.8202 (m) REVERT: A 737 ASP cc_start: 0.8233 (t0) cc_final: 0.7757 (t0) REVERT: B 306 ILE cc_start: 0.8278 (mp) cc_final: 0.8046 (mt) REVERT: B 629 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 686 GLN cc_start: 0.8387 (mp10) cc_final: 0.8134 (mp10) REVERT: B 689 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8486 (ttp) REVERT: B 701 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8606 (mmmm) REVERT: C 607 MET cc_start: 0.8677 (mtp) cc_final: 0.8427 (mtm) REVERT: C 670 ASP cc_start: 0.8102 (m-30) cc_final: 0.7809 (m-30) REVERT: C 689 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8474 (ttp) REVERT: D 526 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8064 (mmtm) REVERT: D 534 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8573 (mtpt) REVERT: D 579 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8557 (tttm) REVERT: D 624 LYS cc_start: 0.8793 (mmpt) cc_final: 0.8502 (mmtm) REVERT: E 318 VAL cc_start: 0.9052 (t) cc_final: 0.8834 (p) REVERT: E 325 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 541 ILE cc_start: 0.8682 (mt) cc_final: 0.8478 (mp) REVERT: E 624 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8555 (mmtp) REVERT: E 647 ASP cc_start: 0.7959 (m-30) cc_final: 0.7725 (m-30) REVERT: F 574 PHE cc_start: 0.6023 (m-10) cc_final: 0.5721 (m-10) REVERT: F 610 GLU cc_start: 0.8015 (tp30) cc_final: 0.7769 (tp30) REVERT: F 671 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8230 (mmm160) REVERT: F 695 GLU cc_start: 0.8298 (tt0) cc_final: 0.8086 (tt0) REVERT: F 701 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8490 (mtmt) REVERT: F 715 PHE cc_start: 0.8308 (t80) cc_final: 0.8078 (t80) REVERT: F 735 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7816 (mt-10) REVERT: G 530 LYS cc_start: 0.8576 (mttt) cc_final: 0.8218 (mptp) REVERT: G 531 GLN cc_start: 0.8238 (mt0) cc_final: 0.7867 (mt0) REVERT: G 534 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8834 (mttp) REVERT: G 545 ILE cc_start: 0.8646 (mp) cc_final: 0.8393 (mp) REVERT: G 673 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8565 (ttmm) REVERT: G 737 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7713 (t0) REVERT: G 748 SER cc_start: 0.8893 (t) cc_final: 0.8672 (p) outliers start: 81 outliers final: 55 residues processed: 643 average time/residue: 0.5384 time to fit residues: 393.9939 Evaluate side-chains 681 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 619 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 737 ASP Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 9 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107974 restraints weight = 32828.034| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.00 r_work: 0.3310 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20974 Z= 0.154 Angle : 0.564 11.587 28424 Z= 0.285 Chirality : 0.042 0.243 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.091 59.939 2781 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.71 % Allowed : 20.63 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.96 (0.17), residues: 2540 helix: 2.97 (0.12), residues: 1613 sheet: 0.12 (0.27), residues: 341 loop : 0.22 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.013 0.001 TYR D 740 PHE 0.030 0.001 PHE G 301 TRP 0.044 0.002 TRP F 548 HIS 0.006 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00359 (20974) covalent geometry : angle 0.56369 (28424) hydrogen bonds : bond 0.04276 ( 1505) hydrogen bonds : angle 3.90446 ( 4437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 620 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7051 (pmt170) cc_final: 0.6845 (pmt170) REVERT: A 300 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 311 ILE cc_start: 0.8855 (tp) cc_final: 0.8636 (tp) REVERT: A 323 LEU cc_start: 0.8481 (mt) cc_final: 0.8182 (tm) REVERT: A 576 ASN cc_start: 0.8100 (t0) cc_final: 0.7734 (t0) REVERT: A 647 ASP cc_start: 0.8194 (m-30) cc_final: 0.7908 (m-30) REVERT: A 717 GLU cc_start: 0.7718 (tp30) cc_final: 0.7431 (tp30) REVERT: A 723 SER cc_start: 0.8476 (t) cc_final: 0.8208 (m) REVERT: A 737 ASP cc_start: 0.8240 (t0) cc_final: 0.7768 (t0) REVERT: B 629 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 686 GLN cc_start: 0.8398 (mp10) cc_final: 0.8143 (mp10) REVERT: B 689 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (ttp) REVERT: B 701 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8602 (mmmm) REVERT: C 567 LEU cc_start: 0.8603 (tm) cc_final: 0.8399 (tt) REVERT: C 607 MET cc_start: 0.8669 (mtp) cc_final: 0.8418 (mtm) REVERT: C 670 ASP cc_start: 0.8120 (m-30) cc_final: 0.7858 (m-30) REVERT: C 689 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: D 524 ASP cc_start: 0.7026 (t0) cc_final: 0.6805 (t0) REVERT: D 526 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (mmtm) REVERT: D 534 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8564 (mtpt) REVERT: D 579 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8568 (tttm) REVERT: D 624 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8505 (mmtm) REVERT: E 318 VAL cc_start: 0.9050 (t) cc_final: 0.8834 (p) REVERT: E 325 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8561 (pp) REVERT: E 624 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8566 (mmtp) REVERT: E 647 ASP cc_start: 0.7945 (m-30) cc_final: 0.7710 (m-30) REVERT: F 324 LYS cc_start: 0.8512 (mttt) cc_final: 0.8241 (mttt) REVERT: F 574 PHE cc_start: 0.5968 (m-10) cc_final: 0.5730 (m-10) REVERT: F 610 GLU cc_start: 0.8032 (tp30) cc_final: 0.7790 (tp30) REVERT: F 671 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8233 (mmm160) REVERT: F 695 GLU cc_start: 0.8315 (tt0) cc_final: 0.8086 (tt0) REVERT: F 701 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (mtmt) REVERT: F 715 PHE cc_start: 0.8315 (t80) cc_final: 0.8085 (t80) REVERT: F 735 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 530 LYS cc_start: 0.8579 (mttt) cc_final: 0.8217 (mptp) REVERT: G 531 GLN cc_start: 0.8246 (mt0) cc_final: 0.7864 (mt0) REVERT: G 534 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8842 (mttp) REVERT: G 545 ILE cc_start: 0.8812 (mp) cc_final: 0.8560 (mp) REVERT: G 673 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8548 (ttmm) REVERT: G 737 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7717 (t0) REVERT: G 748 SER cc_start: 0.8902 (t) cc_final: 0.8681 (p) outliers start: 80 outliers final: 58 residues processed: 646 average time/residue: 0.5279 time to fit residues: 386.7731 Evaluate side-chains 677 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 612 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 737 ASP Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 253 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106170 restraints weight = 32972.215| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.95 r_work: 0.3318 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20974 Z= 0.145 Angle : 0.586 11.850 28424 Z= 0.293 Chirality : 0.042 0.250 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.047 58.987 2781 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.15 % Allowed : 21.46 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.96 (0.17), residues: 2540 helix: 2.96 (0.12), residues: 1613 sheet: 0.13 (0.27), residues: 341 loop : 0.22 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 296 TYR 0.012 0.001 TYR D 740 PHE 0.026 0.001 PHE D 301 TRP 0.041 0.002 TRP A 316 HIS 0.006 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00332 (20974) covalent geometry : angle 0.58574 (28424) hydrogen bonds : bond 0.04227 ( 1505) hydrogen bonds : angle 3.91417 ( 4437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 605 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7013 (pmt170) cc_final: 0.6801 (pmt170) REVERT: A 300 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 311 ILE cc_start: 0.8834 (tp) cc_final: 0.8629 (tp) REVERT: A 323 LEU cc_start: 0.8466 (mt) cc_final: 0.8196 (tm) REVERT: A 526 LYS cc_start: 0.8201 (mttt) cc_final: 0.7993 (mmmm) REVERT: A 576 ASN cc_start: 0.8105 (t0) cc_final: 0.7750 (t0) REVERT: A 647 ASP cc_start: 0.8188 (m-30) cc_final: 0.7900 (m-30) REVERT: A 717 GLU cc_start: 0.7720 (tp30) cc_final: 0.7467 (tp30) REVERT: A 723 SER cc_start: 0.8466 (t) cc_final: 0.8206 (m) REVERT: A 737 ASP cc_start: 0.8206 (t0) cc_final: 0.7722 (t0) REVERT: B 567 LEU cc_start: 0.8426 (tm) cc_final: 0.8171 (tt) REVERT: B 629 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8253 (t80) REVERT: B 686 GLN cc_start: 0.8387 (mp10) cc_final: 0.8133 (mp10) REVERT: B 689 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8490 (ttp) REVERT: B 701 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8606 (mmmm) REVERT: C 317 LEU cc_start: 0.8972 (tp) cc_final: 0.8729 (tm) REVERT: C 567 LEU cc_start: 0.8600 (tm) cc_final: 0.8395 (tt) REVERT: C 607 MET cc_start: 0.8667 (mtp) cc_final: 0.8419 (mtm) REVERT: C 670 ASP cc_start: 0.8118 (m-30) cc_final: 0.7857 (m-30) REVERT: C 689 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: D 524 ASP cc_start: 0.7020 (t0) cc_final: 0.6801 (t0) REVERT: D 526 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8086 (mmtm) REVERT: D 534 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8556 (mtpt) REVERT: D 579 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8558 (tttm) REVERT: D 624 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8510 (mmtm) REVERT: E 318 VAL cc_start: 0.9022 (t) cc_final: 0.8802 (p) REVERT: E 325 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8565 (pp) REVERT: E 624 LYS cc_start: 0.8774 (mmtm) cc_final: 0.8557 (mmtp) REVERT: E 647 ASP cc_start: 0.7934 (m-30) cc_final: 0.7698 (m-30) REVERT: F 324 LYS cc_start: 0.8525 (mttt) cc_final: 0.8283 (mttt) REVERT: F 567 LEU cc_start: 0.8546 (tm) cc_final: 0.8320 (tt) REVERT: F 610 GLU cc_start: 0.8013 (tp30) cc_final: 0.7758 (tp30) REVERT: F 671 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8242 (mmm160) REVERT: F 695 GLU cc_start: 0.8317 (tt0) cc_final: 0.8084 (tt0) REVERT: F 701 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8493 (mtmt) REVERT: F 735 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7840 (mt-10) REVERT: G 530 LYS cc_start: 0.8587 (mttt) cc_final: 0.8210 (mptp) REVERT: G 531 GLN cc_start: 0.8239 (mt0) cc_final: 0.7829 (mt0) REVERT: G 534 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8833 (mttp) REVERT: G 545 ILE cc_start: 0.8769 (mp) cc_final: 0.8542 (mp) REVERT: G 673 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8541 (ttmm) REVERT: G 737 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7737 (t0) outliers start: 68 outliers final: 50 residues processed: 628 average time/residue: 0.5659 time to fit residues: 402.3592 Evaluate side-chains 656 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 600 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 737 ASP Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 163 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108560 restraints weight = 32868.671| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.99 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20974 Z= 0.135 Angle : 0.582 12.298 28424 Z= 0.292 Chirality : 0.041 0.248 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.000 58.320 2781 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.29 % Allowed : 21.60 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.97 (0.17), residues: 2540 helix: 2.97 (0.12), residues: 1614 sheet: 0.11 (0.27), residues: 341 loop : 0.21 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.010 0.001 TYR D 740 PHE 0.032 0.001 PHE G 301 TRP 0.040 0.002 TRP A 316 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00304 (20974) covalent geometry : angle 0.58186 (28424) hydrogen bonds : bond 0.04158 ( 1505) hydrogen bonds : angle 3.89961 ( 4437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9974.10 seconds wall clock time: 169 minutes 47.57 seconds (10187.57 seconds total)