Starting phenix.real_space_refine on Wed Jun 18 03:41:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5d_24186/06_2025/7n5d_24186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5d_24186/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5d_24186/06_2025/7n5d_24186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5d_24186/06_2025/7n5d_24186.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5d_24186/06_2025/7n5d_24186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5d_24186/06_2025/7n5d_24186.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: {'PHE:plan': 3, 'GLU:plan': 1, '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: 12.78, per 1000 atoms: 0.62 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: 4.94 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.07 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: 6.77 Time building geometry restraints manager: 5.70 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 751 or resid 801)) selection = (chain 'B' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 186 through 285 or resid 294 through 751 or resid 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: 1.070 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 45.850 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.090 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.008 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.005 PHE A 335 TYR 0.044 0.008 TYR E 675 ARG 0.006 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.13890 ( 1505) hydrogen bonds : angle 5.98927 ( 4437) covalent geometry : bond 0.02258 (20974) covalent geometry : angle 1.52089 (28424) *********************** 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 : 2.167 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: 1.5542 time to fit residues: 1399.5956 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 : 3.987 ------------------------------------------------------------------------------- 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 219 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 C 698 ASN D 291 GLN D 525 ASN D 576 ASN D 687 HIS D 713 GLN E 533 ASN E 648 GLN E 698 ASN F 345 HIS F 525 ASN F 648 GLN G 533 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107711 restraints weight = 33055.023| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.86 r_work: 0.3307 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20974 Z= 0.165 Angle : 0.594 9.285 28424 Z= 0.309 Chirality : 0.043 0.303 3452 Planarity : 0.004 0.043 3469 Dihedral : 7.080 58.785 2793 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.80 % Allowed : 13.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.16), residues: 2540 helix: 2.52 (0.12), residues: 1612 sheet: 0.57 (0.29), residues: 299 loop : 0.71 (0.27), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 273 HIS 0.007 0.001 HIS A 592 PHE 0.024 0.002 PHE D 301 TYR 0.009 0.002 TYR C 629 ARG 0.005 0.001 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 1505) hydrogen bonds : angle 4.24639 ( 4437) covalent geometry : bond 0.00360 (20974) covalent geometry : angle 0.59388 (28424) *********************** 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 772 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 690 time to evaluate : 2.271 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 302 VAL cc_start: 0.8693 (t) cc_final: 0.8475 (m) REVERT: A 316 TRP cc_start: 0.7885 (t-100) cc_final: 0.7665 (t-100) REVERT: A 330 PHE cc_start: 0.7786 (t80) cc_final: 0.7532 (t80) REVERT: A 576 ASN cc_start: 0.7985 (t0) cc_final: 0.7426 (t0) REVERT: A 647 ASP cc_start: 0.8125 (m-30) cc_final: 0.7895 (m-30) REVERT: A 723 SER cc_start: 0.8508 (t) cc_final: 0.8221 (m) REVERT: A 737 ASP cc_start: 0.8226 (t0) cc_final: 0.7922 (t0) REVERT: B 324 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7929 (mmtt) REVERT: B 328 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8531 (t) REVERT: B 530 LYS cc_start: 0.8616 (mptt) cc_final: 0.8395 (mttp) REVERT: B 568 VAL cc_start: 0.8530 (p) cc_final: 0.8310 (p) REVERT: B 583 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8382 (mt-10) REVERT: B 686 GLN cc_start: 0.8362 (mp-120) cc_final: 0.7865 (mp10) REVERT: C 579 LYS cc_start: 0.8877 (tmmm) cc_final: 0.8665 (tttp) REVERT: D 307 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8483 (m) REVERT: D 314 PHE cc_start: 0.8061 (t80) cc_final: 0.7827 (t80) REVERT: D 714 ASP cc_start: 0.8249 (t0) cc_final: 0.8029 (t0) REVERT: D 737 ASP cc_start: 0.8248 (t0) cc_final: 0.7938 (t0) REVERT: D 739 LYS cc_start: 0.8630 (mttp) cc_final: 0.8374 (mttp) REVERT: E 318 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8814 (p) REVERT: E 530 LYS cc_start: 0.8811 (mttt) cc_final: 0.8606 (mmmm) REVERT: E 624 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8493 (mmtp) REVERT: F 324 LYS cc_start: 0.8359 (mttm) cc_final: 0.8155 (mttm) REVERT: F 572 PHE cc_start: 0.7991 (t80) cc_final: 0.7770 (t80) REVERT: F 671 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: F 673 LYS cc_start: 0.8612 (tttt) cc_final: 0.8230 (tttp) REVERT: F 677 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7538 (mt-10) REVERT: F 735 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7684 (mt-10) REVERT: G 324 LYS cc_start: 0.8400 (mttm) cc_final: 0.8119 (mttm) REVERT: G 530 LYS cc_start: 0.8633 (mttt) cc_final: 0.8324 (mttp) REVERT: G 534 LYS cc_start: 0.9203 (mttt) cc_final: 0.8993 (mttp) REVERT: G 561 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8069 (m) REVERT: G 715 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: G 737 ASP cc_start: 0.8029 (t0) cc_final: 0.7798 (t0) REVERT: G 748 SER cc_start: 0.8937 (t) cc_final: 0.8641 (p) outliers start: 82 outliers final: 27 residues processed: 716 average time/residue: 1.2559 time to fit residues: 1030.8261 Evaluate side-chains 684 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 652 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 748 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 328 SER 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 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 86 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 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 513 ASN A 533 ASN A 605 ASN A 686 GLN B 576 ASN B 686 GLN C 648 GLN C 698 ASN C 713 GLN D 291 GLN D 648 GLN D 698 ASN D 719 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN F 688 ASN G 576 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106044 restraints weight = 32741.978| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.95 r_work: 0.3304 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2991 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= 0.150 Angle : 0.534 7.990 28424 Z= 0.278 Chirality : 0.042 0.266 3452 Planarity : 0.003 0.040 3469 Dihedral : 6.832 58.324 2785 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.94 % Allowed : 17.01 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.16), residues: 2540 helix: 2.68 (0.12), residues: 1613 sheet: 0.54 (0.28), residues: 299 loop : 0.41 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 273 HIS 0.006 0.001 HIS A 592 PHE 0.026 0.002 PHE F 301 TYR 0.012 0.001 TYR E 740 ARG 0.007 0.000 ARG B 720 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 1505) hydrogen bonds : angle 4.04053 ( 4437) covalent geometry : bond 0.00335 (20974) covalent geometry : angle 0.53371 (28424) *********************** 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 : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 311 ILE cc_start: 0.8889 (tp) cc_final: 0.8674 (tp) REVERT: A 526 LYS cc_start: 0.8217 (mttt) cc_final: 0.7927 (ttmm) REVERT: A 576 ASN cc_start: 0.8035 (t0) cc_final: 0.7600 (t0) REVERT: A 647 ASP cc_start: 0.8151 (m-30) cc_final: 0.7892 (m-30) REVERT: A 717 GLU cc_start: 0.7903 (tp30) cc_final: 0.7555 (tp30) REVERT: A 723 SER cc_start: 0.8493 (t) cc_final: 0.8250 (m) REVERT: A 737 ASP cc_start: 0.8228 (t0) cc_final: 0.7889 (t0) REVERT: B 324 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8081 (mmtt) REVERT: B 583 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8316 (mt-10) REVERT: B 657 ASP cc_start: 0.8281 (t70) cc_final: 0.8074 (t70) REVERT: B 686 GLN cc_start: 0.8384 (mp10) cc_final: 0.7905 (mp10) REVERT: C 526 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7670 (mmtt) REVERT: C 579 LYS cc_start: 0.8889 (tmmm) cc_final: 0.8689 (tttm) REVERT: C 713 GLN cc_start: 0.8300 (tp40) cc_final: 0.7687 (tp40) REVERT: D 282 VAL cc_start: 0.7979 (p) cc_final: 0.7737 (m) REVERT: D 314 PHE cc_start: 0.8101 (t80) cc_final: 0.7893 (t80) REVERT: D 526 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8135 (mmtm) REVERT: D 534 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8623 (mtpt) REVERT: D 579 LYS cc_start: 0.8819 (tmmm) cc_final: 0.8547 (tttm) REVERT: D 664 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7801 (tptm) REVERT: D 737 ASP cc_start: 0.8299 (t0) cc_final: 0.7929 (t0) REVERT: D 739 LYS cc_start: 0.8647 (mttp) cc_final: 0.8344 (mttp) REVERT: E 318 VAL cc_start: 0.9057 (t) cc_final: 0.8820 (p) REVERT: E 325 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8579 (pp) REVERT: E 530 LYS cc_start: 0.8693 (mttt) cc_final: 0.8447 (mtmm) REVERT: E 583 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8206 (mt-10) REVERT: E 624 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8564 (mmtp) REVERT: F 548 TRP cc_start: 0.8261 (t60) cc_final: 0.7737 (t60) REVERT: F 671 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: F 701 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8509 (mtmt) REVERT: F 735 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7711 (mt-10) REVERT: G 324 LYS cc_start: 0.8540 (mttm) cc_final: 0.8188 (mttm) REVERT: G 530 LYS cc_start: 0.8616 (mttt) cc_final: 0.8267 (mttp) REVERT: G 534 LYS cc_start: 0.9136 (mttt) cc_final: 0.8925 (mttp) REVERT: G 545 ILE cc_start: 0.8786 (mp) cc_final: 0.8520 (mp) REVERT: G 737 ASP cc_start: 0.8086 (t0) cc_final: 0.7836 (t0) REVERT: G 748 SER cc_start: 0.8935 (t) cc_final: 0.8650 (p) outliers start: 85 outliers final: 45 residues processed: 682 average time/residue: 1.1763 time to fit residues: 915.0032 Evaluate side-chains 674 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 625 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN 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 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 606 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 318 VAL 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 549 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 562 LEU 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 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 526 LYS Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 38 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 513 ASN A 686 GLN B 576 ASN C 648 GLN D 576 ASN E 531 GLN E 648 GLN E 688 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN F 688 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106031 restraints weight = 32989.606| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.96 r_work: 0.3308 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20974 Z= 0.136 Angle : 0.517 11.566 28424 Z= 0.265 Chirality : 0.042 0.312 3452 Planarity : 0.003 0.051 3469 Dihedral : 6.493 56.651 2781 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.76 % Allowed : 19.19 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.17), residues: 2540 helix: 2.82 (0.12), residues: 1613 sheet: 0.23 (0.27), residues: 341 loop : 0.39 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 548 HIS 0.005 0.001 HIS E 708 PHE 0.021 0.001 PHE A 271 TYR 0.009 0.001 TYR E 740 ARG 0.004 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 1505) hydrogen bonds : angle 3.94137 ( 4437) covalent geometry : bond 0.00305 (20974) covalent geometry : angle 0.51665 (28424) *********************** 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 707 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 626 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7110 (pmt170) cc_final: 0.6901 (pmt170) REVERT: A 300 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 311 ILE cc_start: 0.8865 (tp) cc_final: 0.8642 (tp) REVERT: A 576 ASN cc_start: 0.8042 (t0) cc_final: 0.7725 (t0) REVERT: A 647 ASP cc_start: 0.8162 (m-30) cc_final: 0.7886 (m-30) REVERT: A 717 GLU cc_start: 0.7838 (tp30) cc_final: 0.7531 (tp30) REVERT: A 723 SER cc_start: 0.8459 (t) cc_final: 0.8199 (m) REVERT: A 737 ASP cc_start: 0.8245 (t0) cc_final: 0.7763 (t0) REVERT: B 583 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 686 GLN cc_start: 0.8404 (mp10) cc_final: 0.7914 (mp10) REVERT: C 670 ASP cc_start: 0.8134 (m-30) cc_final: 0.7919 (m-30) REVERT: D 526 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8128 (mmtm) REVERT: D 534 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8609 (mtpt) REVERT: D 579 LYS cc_start: 0.8795 (tmmm) cc_final: 0.8587 (ttpp) REVERT: D 664 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7834 (tptm) REVERT: D 737 ASP cc_start: 0.8288 (t0) cc_final: 0.7833 (t0) REVERT: D 739 LYS cc_start: 0.8587 (mttp) cc_final: 0.8191 (mttp) REVERT: E 318 VAL cc_start: 0.9051 (t) cc_final: 0.8818 (p) REVERT: E 325 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8557 (pp) REVERT: E 530 LYS cc_start: 0.8660 (mttt) cc_final: 0.8459 (mmmm) REVERT: E 624 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8556 (mmtp) REVERT: F 548 TRP cc_start: 0.8204 (t60) cc_final: 0.7832 (t60) REVERT: F 671 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8277 (mmm-85) REVERT: F 701 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8523 (mtmt) REVERT: F 715 PHE cc_start: 0.8322 (t80) cc_final: 0.8082 (t80) REVERT: F 735 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7795 (mt-10) REVERT: G 324 LYS cc_start: 0.8588 (mttm) cc_final: 0.8372 (mttm) REVERT: G 530 LYS cc_start: 0.8592 (mttt) cc_final: 0.8249 (mttp) REVERT: G 534 LYS cc_start: 0.9125 (mttt) cc_final: 0.8919 (mttp) REVERT: G 545 ILE cc_start: 0.8754 (mp) cc_final: 0.8469 (mp) REVERT: G 715 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: G 737 ASP cc_start: 0.8055 (t0) cc_final: 0.7803 (t0) REVERT: G 748 SER cc_start: 0.8915 (t) cc_final: 0.8660 (p) outliers start: 81 outliers final: 48 residues processed: 657 average time/residue: 1.2109 time to fit residues: 902.9966 Evaluate side-chains 674 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 621 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 515 GLN 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 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 629 TYR Chi-restraints excluded: chain C residue 325 ILE 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 299 LEU Chi-restraints excluded: chain D residue 300 GLU 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 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 266 THR 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 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 626 LYS 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 167 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 67 optimal weight: 0.0870 chunk 95 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 533 ASN A 686 GLN B 613 ASN C 648 GLN D 531 GLN E 648 GLN E 688 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106217 restraints weight = 33016.832| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.98 r_work: 0.3325 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20974 Z= 0.123 Angle : 0.506 10.893 28424 Z= 0.258 Chirality : 0.041 0.311 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.335 59.699 2781 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.31 % Allowed : 19.05 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.17), residues: 2540 helix: 2.93 (0.12), residues: 1613 sheet: 0.21 (0.27), residues: 331 loop : 0.30 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 548 HIS 0.004 0.001 HIS A 592 PHE 0.025 0.001 PHE G 301 TYR 0.007 0.001 TYR E 740 ARG 0.003 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 1505) hydrogen bonds : angle 3.87916 ( 4437) covalent geometry : bond 0.00272 (20974) covalent geometry : angle 0.50620 (28424) *********************** 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 712 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 619 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7023 (pmt170) cc_final: 0.6807 (pmt170) REVERT: A 300 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 311 ILE cc_start: 0.8869 (tp) cc_final: 0.8636 (OUTLIER) REVERT: A 323 LEU cc_start: 0.8480 (mt) cc_final: 0.8134 (tm) REVERT: A 526 LYS cc_start: 0.8183 (mttt) cc_final: 0.7912 (ttmm) REVERT: A 576 ASN cc_start: 0.8031 (t0) cc_final: 0.7658 (t0) REVERT: A 579 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8131 (ttpt) REVERT: A 647 ASP cc_start: 0.8176 (m-30) cc_final: 0.7900 (m-30) REVERT: A 717 GLU cc_start: 0.7809 (tp30) cc_final: 0.7497 (tp30) REVERT: A 723 SER cc_start: 0.8457 (t) cc_final: 0.8207 (m) REVERT: A 737 ASP cc_start: 0.8198 (t0) cc_final: 0.7757 (t0) REVERT: B 324 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 583 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 629 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 686 GLN cc_start: 0.8391 (mp10) cc_final: 0.8147 (mp10) REVERT: B 689 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (ttp) REVERT: C 670 ASP cc_start: 0.8111 (m-30) cc_final: 0.7863 (m-30) REVERT: C 735 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 526 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8089 (mmtm) REVERT: D 534 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8631 (mtpt) REVERT: D 548 TRP cc_start: 0.7583 (t60) cc_final: 0.6992 (t60) REVERT: D 664 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7787 (tptm) REVERT: D 701 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8600 (mmtp) REVERT: D 723 SER cc_start: 0.8457 (t) cc_final: 0.8232 (p) REVERT: D 737 ASP cc_start: 0.8288 (t0) cc_final: 0.7787 (t0) REVERT: D 739 LYS cc_start: 0.8592 (mttp) cc_final: 0.8145 (mttp) REVERT: E 318 VAL cc_start: 0.9048 (t) cc_final: 0.8825 (p) REVERT: E 325 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8545 (pp) REVERT: E 624 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8564 (mmtp) REVERT: F 548 TRP cc_start: 0.8186 (t60) cc_final: 0.7958 (t60) REVERT: F 671 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: F 695 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 701 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8508 (mtmt) REVERT: F 715 PHE cc_start: 0.8313 (t80) cc_final: 0.8083 (t80) REVERT: F 735 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7651 (mt-10) REVERT: G 324 LYS cc_start: 0.8560 (mttm) cc_final: 0.8316 (mttm) REVERT: G 530 LYS cc_start: 0.8597 (mttt) cc_final: 0.8253 (mttp) REVERT: G 545 ILE cc_start: 0.8705 (mp) cc_final: 0.8437 (mp) REVERT: G 737 ASP cc_start: 0.8044 (t0) cc_final: 0.7764 (t0) REVERT: G 748 SER cc_start: 0.8904 (t) cc_final: 0.8664 (p) outliers start: 93 outliers final: 51 residues processed: 653 average time/residue: 1.2676 time to fit residues: 943.4737 Evaluate side-chains 672 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 615 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL 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 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 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 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 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 547 ILE Chi-restraints excluded: chain D residue 559 LEU 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 664 LYS 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 662 VAL 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 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 625 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 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 213 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 184 optimal weight: 0.0170 chunk 219 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN B 576 ASN B 613 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106980 restraints weight = 32976.148| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.95 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20974 Z= 0.124 Angle : 0.511 9.848 28424 Z= 0.259 Chirality : 0.041 0.260 3452 Planarity : 0.003 0.034 3469 Dihedral : 6.227 59.150 2781 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.99 % Allowed : 19.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.17), residues: 2540 helix: 2.99 (0.12), residues: 1613 sheet: 0.21 (0.27), residues: 341 loop : 0.29 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 548 HIS 0.004 0.001 HIS A 592 PHE 0.022 0.001 PHE A 271 TYR 0.010 0.001 TYR D 740 ARG 0.003 0.000 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1505) hydrogen bonds : angle 3.84457 ( 4437) covalent geometry : bond 0.00274 (20974) covalent geometry : angle 0.51121 (28424) *********************** 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 716 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 630 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6999 (pmt170) cc_final: 0.6786 (pmt170) REVERT: A 300 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 311 ILE cc_start: 0.8868 (tp) cc_final: 0.8633 (tp) REVERT: A 323 LEU cc_start: 0.8481 (mt) cc_final: 0.8139 (tm) REVERT: A 526 LYS cc_start: 0.8192 (mttt) cc_final: 0.7918 (ttmm) REVERT: A 576 ASN cc_start: 0.8078 (t0) cc_final: 0.7750 (t0) REVERT: A 579 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8143 (ttpt) REVERT: A 621 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8509 (mtmt) REVERT: A 647 ASP cc_start: 0.8174 (m-30) cc_final: 0.7882 (m-30) REVERT: A 717 GLU cc_start: 0.7801 (tp30) cc_final: 0.7473 (tp30) REVERT: A 723 SER cc_start: 0.8441 (t) cc_final: 0.8192 (m) REVERT: A 737 ASP cc_start: 0.8175 (t0) cc_final: 0.7718 (t0) REVERT: B 324 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8007 (mmtt) REVERT: B 629 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8185 (t80) REVERT: B 686 GLN cc_start: 0.8388 (mp10) cc_final: 0.8136 (mp10) REVERT: B 689 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: B 697 VAL cc_start: 0.7855 (m) cc_final: 0.7652 (t) REVERT: C 300 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: C 670 ASP cc_start: 0.8121 (m-30) cc_final: 0.7862 (m-30) REVERT: D 526 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8090 (mmtm) REVERT: D 534 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8620 (mtpt) REVERT: D 548 TRP cc_start: 0.7599 (t60) cc_final: 0.7039 (t60) REVERT: D 579 LYS cc_start: 0.8817 (tmmt) cc_final: 0.8608 (ttpp) REVERT: D 624 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8514 (mmtm) REVERT: D 664 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7799 (tptm) REVERT: D 701 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (mmtp) REVERT: D 723 SER cc_start: 0.8424 (t) cc_final: 0.8207 (p) REVERT: D 737 ASP cc_start: 0.8273 (t0) cc_final: 0.8065 (t0) REVERT: E 283 MET cc_start: 0.6611 (tpp) cc_final: 0.6024 (mpp) REVERT: E 318 VAL cc_start: 0.9053 (t) cc_final: 0.8826 (p) REVERT: E 325 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 624 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8545 (mmtp) REVERT: E 739 LYS cc_start: 0.8767 (mttp) cc_final: 0.8455 (mttp) REVERT: F 548 TRP cc_start: 0.8211 (t60) cc_final: 0.7993 (t60) REVERT: F 671 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: F 695 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7716 (tm-30) REVERT: F 701 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mtmt) REVERT: F 715 PHE cc_start: 0.8291 (t80) cc_final: 0.8064 (t80) REVERT: F 735 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7660 (mt-10) REVERT: G 530 LYS cc_start: 0.8546 (mttt) cc_final: 0.8218 (mttp) REVERT: G 545 ILE cc_start: 0.8675 (mp) cc_final: 0.8414 (mp) REVERT: G 673 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8565 (ttmm) REVERT: G 737 ASP cc_start: 0.8037 (t0) cc_final: 0.7721 (t0) REVERT: G 748 SER cc_start: 0.8895 (t) cc_final: 0.8656 (p) outliers start: 86 outliers final: 47 residues processed: 660 average time/residue: 1.2921 time to fit residues: 967.9899 Evaluate side-chains 675 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 620 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN 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 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 629 TYR 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 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 300 GLU Chi-restraints excluded: chain D residue 526 LYS 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 664 LYS 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 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 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 624 LYS Chi-restraints excluded: chain F residue 625 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 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 8 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN B 613 ASN C 648 GLN E 648 GLN E 688 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 GLN 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 = 0.3864 r_free = 0.3864 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106034 restraints weight = 32970.371| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.95 r_work: 0.3318 rms_B_bonded: 2.66 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: 0.8023 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20974 Z= 0.137 Angle : 0.516 8.892 28424 Z= 0.264 Chirality : 0.041 0.245 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.159 59.957 2781 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.94 % Allowed : 19.94 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.17), residues: 2540 helix: 2.99 (0.12), residues: 1613 sheet: 0.21 (0.27), residues: 341 loop : 0.26 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 548 HIS 0.005 0.001 HIS E 708 PHE 0.028 0.001 PHE G 301 TYR 0.011 0.001 TYR D 740 ARG 0.003 0.000 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1505) hydrogen bonds : angle 3.85002 ( 4437) covalent geometry : bond 0.00314 (20974) covalent geometry : angle 0.51599 (28424) *********************** 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 705 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 620 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7013 (pmt170) cc_final: 0.6805 (pmt170) REVERT: A 300 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 311 ILE cc_start: 0.8853 (tp) cc_final: 0.8634 (tp) REVERT: A 323 LEU cc_start: 0.8479 (mt) cc_final: 0.8130 (tm) REVERT: A 526 LYS cc_start: 0.8297 (mttt) cc_final: 0.8063 (mmmm) REVERT: A 576 ASN cc_start: 0.8099 (t0) cc_final: 0.7767 (t0) REVERT: A 579 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8166 (ttpt) REVERT: A 647 ASP cc_start: 0.8195 (m-30) cc_final: 0.7920 (m-30) REVERT: A 717 GLU cc_start: 0.7822 (tp30) cc_final: 0.7491 (tp30) REVERT: A 723 SER cc_start: 0.8459 (t) cc_final: 0.8202 (m) REVERT: A 737 ASP cc_start: 0.8180 (t0) cc_final: 0.7722 (t0) REVERT: B 324 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8010 (mmtt) REVERT: B 629 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 686 GLN cc_start: 0.8385 (mp10) cc_final: 0.8134 (mp10) REVERT: B 689 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: B 697 VAL cc_start: 0.7916 (m) cc_final: 0.7715 (t) REVERT: C 283 MET cc_start: 0.6135 (mmm) cc_final: 0.5888 (mmm) REVERT: C 300 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 317 LEU cc_start: 0.8982 (tp) cc_final: 0.8752 (tm) REVERT: C 567 LEU cc_start: 0.8606 (tm) cc_final: 0.8406 (tt) REVERT: C 670 ASP cc_start: 0.8126 (m-30) cc_final: 0.7844 (m-30) REVERT: D 526 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8103 (mmtm) REVERT: D 534 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8612 (mtpt) REVERT: D 579 LYS cc_start: 0.8837 (tmmt) cc_final: 0.8614 (ttpp) REVERT: D 624 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8518 (mmtm) REVERT: D 664 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (tptm) REVERT: E 283 MET cc_start: 0.6594 (tpp) cc_final: 0.6039 (mpp) REVERT: E 318 VAL cc_start: 0.9053 (t) cc_final: 0.8835 (p) REVERT: E 325 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8545 (pp) REVERT: E 541 ILE cc_start: 0.8669 (mt) cc_final: 0.8465 (mp) REVERT: E 579 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8447 (tmtp) REVERT: E 624 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8565 (mmtp) REVERT: E 647 ASP cc_start: 0.7944 (m-30) cc_final: 0.7716 (m-30) REVERT: F 574 PHE cc_start: 0.6150 (m-10) cc_final: 0.5726 (m-10) REVERT: F 671 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8197 (mmm160) REVERT: F 695 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7687 (tm-30) REVERT: F 715 PHE cc_start: 0.8295 (t80) cc_final: 0.8064 (t80) REVERT: F 735 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7624 (mt-10) REVERT: G 530 LYS cc_start: 0.8530 (mttt) cc_final: 0.8210 (mptp) REVERT: G 673 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8564 (ttmm) REVERT: G 715 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: G 737 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7669 (t0) REVERT: G 748 SER cc_start: 0.8895 (t) cc_final: 0.8662 (p) outliers start: 85 outliers final: 56 residues processed: 648 average time/residue: 1.2253 time to fit residues: 901.8972 Evaluate side-chains 675 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 610 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 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 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 629 TYR 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 324 LYS Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 ILE 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 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR 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 664 LYS 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 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 543 MET 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 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 715 PHE 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 153 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 648 GLN F 688 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105883 restraints weight = 32963.489| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.95 r_work: 0.3317 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20974 Z= 0.138 Angle : 0.548 11.316 28424 Z= 0.275 Chirality : 0.041 0.280 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.115 59.383 2781 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.76 % Allowed : 20.35 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 2540 helix: 3.00 (0.12), residues: 1614 sheet: 0.21 (0.27), residues: 341 loop : 0.27 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 548 HIS 0.005 0.001 HIS E 708 PHE 0.023 0.001 PHE A 271 TYR 0.011 0.001 TYR D 740 ARG 0.003 0.000 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 1505) hydrogen bonds : angle 3.85631 ( 4437) covalent geometry : bond 0.00314 (20974) covalent geometry : angle 0.54824 (28424) *********************** 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 696 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 615 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 311 ILE cc_start: 0.8884 (tp) cc_final: 0.8675 (tp) REVERT: A 323 LEU cc_start: 0.8465 (mt) cc_final: 0.8109 (tm) REVERT: A 526 LYS cc_start: 0.8250 (mttt) cc_final: 0.8030 (mmmm) REVERT: A 576 ASN cc_start: 0.8136 (t0) cc_final: 0.7778 (t0) REVERT: A 579 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8185 (ttpt) REVERT: A 647 ASP cc_start: 0.8187 (m-30) cc_final: 0.7907 (m-30) REVERT: A 717 GLU cc_start: 0.7847 (tp30) cc_final: 0.7522 (tp30) REVERT: A 723 SER cc_start: 0.8454 (t) cc_final: 0.8205 (m) REVERT: A 737 ASP cc_start: 0.8195 (t0) cc_final: 0.7724 (t0) REVERT: B 324 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8113 (mmtt) REVERT: B 624 LYS cc_start: 0.8769 (mptp) cc_final: 0.8548 (mmtp) REVERT: B 629 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8227 (t80) REVERT: B 686 GLN cc_start: 0.8386 (mp10) cc_final: 0.8138 (mp10) REVERT: B 689 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: B 697 VAL cc_start: 0.7965 (m) cc_final: 0.7756 (t) REVERT: C 283 MET cc_start: 0.5993 (mmm) cc_final: 0.5744 (mmm) REVERT: C 670 ASP cc_start: 0.8156 (m-30) cc_final: 0.7900 (m-30) REVERT: D 526 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8090 (mmtm) REVERT: D 534 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8639 (mtpt) REVERT: D 548 TRP cc_start: 0.7653 (t60) cc_final: 0.7057 (t60) REVERT: D 579 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8598 (ttpp) REVERT: D 624 LYS cc_start: 0.8800 (mmpt) cc_final: 0.8519 (mmtm) REVERT: D 664 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7819 (tptm) REVERT: E 283 MET cc_start: 0.6609 (tpp) cc_final: 0.6089 (mpp) REVERT: E 318 VAL cc_start: 0.9058 (t) cc_final: 0.8845 (p) REVERT: E 325 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8562 (pp) REVERT: E 541 ILE cc_start: 0.8687 (mt) cc_final: 0.8476 (mp) REVERT: E 624 LYS cc_start: 0.8774 (mmtm) cc_final: 0.8542 (mmpt) REVERT: E 647 ASP cc_start: 0.7952 (m-30) cc_final: 0.7724 (m-30) REVERT: F 548 TRP cc_start: 0.8282 (t60) cc_final: 0.7991 (t60) REVERT: F 574 PHE cc_start: 0.6053 (m-10) cc_final: 0.5722 (m-10) REVERT: F 671 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8223 (mmm160) REVERT: F 695 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 715 PHE cc_start: 0.8286 (t80) cc_final: 0.8051 (t80) REVERT: F 735 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7669 (mt-10) REVERT: G 530 LYS cc_start: 0.8533 (mttt) cc_final: 0.8237 (mptp) REVERT: G 673 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8581 (ttmm) REVERT: G 737 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7686 (t0) REVERT: G 748 SER cc_start: 0.8888 (t) cc_final: 0.8679 (p) outliers start: 81 outliers final: 54 residues processed: 643 average time/residue: 1.2537 time to fit residues: 920.4613 Evaluate side-chains 680 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 620 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU 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 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE 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 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 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 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 664 LYS 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 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 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 739 LYS Chi-restraints excluded: chain G residue 324 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 42 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 254 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 198 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN D 531 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 GLN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106832 restraints weight = 33064.843| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.96 r_work: 0.3329 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20974 Z= 0.125 Angle : 0.552 12.260 28424 Z= 0.280 Chirality : 0.042 0.328 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.064 59.757 2781 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.25 % Allowed : 20.91 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2540 helix: 3.02 (0.12), residues: 1614 sheet: 0.21 (0.27), residues: 341 loop : 0.25 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 548 HIS 0.004 0.001 HIS E 708 PHE 0.029 0.001 PHE G 301 TYR 0.010 0.001 TYR D 740 ARG 0.005 0.000 ARG D 296 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 1505) hydrogen bonds : angle 3.87245 ( 4437) covalent geometry : bond 0.00278 (20974) covalent geometry : angle 0.55201 (28424) *********************** 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 683 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 613 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6934 (pmt170) cc_final: 0.6655 (pmt170) REVERT: A 300 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 311 ILE cc_start: 0.8859 (tp) cc_final: 0.8644 (tp) REVERT: A 323 LEU cc_start: 0.8447 (mt) cc_final: 0.8097 (tm) REVERT: A 576 ASN cc_start: 0.8088 (t0) cc_final: 0.7725 (t0) REVERT: A 647 ASP cc_start: 0.8175 (m-30) cc_final: 0.7892 (m-30) REVERT: A 717 GLU cc_start: 0.7798 (tp30) cc_final: 0.7470 (tp30) REVERT: A 723 SER cc_start: 0.8452 (t) cc_final: 0.8199 (m) REVERT: A 737 ASP cc_start: 0.8165 (t0) cc_final: 0.7682 (t0) REVERT: B 567 LEU cc_start: 0.8435 (tm) cc_final: 0.8184 (tt) REVERT: B 629 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8183 (t80) REVERT: B 686 GLN cc_start: 0.8388 (mp10) cc_final: 0.8128 (mp10) REVERT: B 689 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8498 (ttp) REVERT: B 697 VAL cc_start: 0.7926 (m) cc_final: 0.7709 (t) REVERT: C 317 LEU cc_start: 0.8968 (tp) cc_final: 0.8726 (tm) REVERT: C 670 ASP cc_start: 0.8130 (m-30) cc_final: 0.7838 (m-30) REVERT: D 524 ASP cc_start: 0.7016 (t0) cc_final: 0.6795 (t0) REVERT: D 526 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8095 (mmtm) REVERT: D 579 LYS cc_start: 0.8834 (tmmt) cc_final: 0.8590 (ttpp) REVERT: D 624 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8505 (mmtm) REVERT: D 664 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7809 (tptm) REVERT: D 701 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8542 (mmtp) REVERT: E 318 VAL cc_start: 0.9048 (t) cc_final: 0.8831 (p) REVERT: E 325 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8577 (pp) REVERT: E 541 ILE cc_start: 0.8688 (mt) cc_final: 0.8476 (mp) REVERT: E 624 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8536 (mmtp) REVERT: E 647 ASP cc_start: 0.7952 (m-30) cc_final: 0.7724 (m-30) REVERT: F 574 PHE cc_start: 0.5947 (m-10) cc_final: 0.5711 (m-10) REVERT: F 671 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8195 (mmm160) REVERT: F 695 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F 715 PHE cc_start: 0.8220 (t80) cc_final: 0.8009 (t80) REVERT: F 735 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7688 (mt-10) REVERT: G 530 LYS cc_start: 0.8513 (mttt) cc_final: 0.8295 (mptp) REVERT: G 673 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8552 (ttmm) REVERT: G 737 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7659 (t0) outliers start: 70 outliers final: 51 residues processed: 639 average time/residue: 1.2284 time to fit residues: 890.1131 Evaluate side-chains 669 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 611 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 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 328 SER 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 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 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 664 LYS 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 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 739 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 187 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN C 648 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 GLN G 525 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108407 restraints weight = 32784.802| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.97 r_work: 0.3324 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20974 Z= 0.140 Angle : 0.583 12.903 28424 Z= 0.291 Chirality : 0.042 0.284 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.040 59.574 2781 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.20 % Allowed : 21.23 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.17), residues: 2540 helix: 2.97 (0.12), residues: 1614 sheet: 0.19 (0.27), residues: 341 loop : 0.25 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 273 HIS 0.005 0.001 HIS E 708 PHE 0.025 0.001 PHE A 271 TYR 0.011 0.001 TYR D 740 ARG 0.003 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 1505) hydrogen bonds : angle 3.89925 ( 4437) covalent geometry : bond 0.00319 (20974) covalent geometry : angle 0.58280 (28424) ********************** 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 680 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 611 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6902 (pmt170) cc_final: 0.6606 (pmt170) REVERT: A 300 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 311 ILE cc_start: 0.8822 (tp) cc_final: 0.8615 (tp) REVERT: A 323 LEU cc_start: 0.8439 (mt) cc_final: 0.8081 (tm) REVERT: A 647 ASP cc_start: 0.8172 (m-30) cc_final: 0.7884 (m-30) REVERT: A 717 GLU cc_start: 0.7830 (tp30) cc_final: 0.7500 (tp30) REVERT: A 723 SER cc_start: 0.8456 (t) cc_final: 0.8210 (m) REVERT: A 737 ASP cc_start: 0.8148 (t0) cc_final: 0.7655 (t0) REVERT: B 567 LEU cc_start: 0.8409 (tm) cc_final: 0.8174 (tt) REVERT: B 629 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 686 GLN cc_start: 0.8385 (mp10) cc_final: 0.8131 (mp10) REVERT: B 689 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8504 (ttp) REVERT: B 697 VAL cc_start: 0.7928 (m) cc_final: 0.7715 (t) REVERT: C 317 LEU cc_start: 0.8976 (tp) cc_final: 0.8731 (tm) REVERT: C 567 LEU cc_start: 0.8598 (tm) cc_final: 0.8395 (tt) REVERT: C 670 ASP cc_start: 0.8129 (m-30) cc_final: 0.7838 (m-30) REVERT: D 524 ASP cc_start: 0.6994 (t0) cc_final: 0.6794 (t0) REVERT: D 526 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8108 (mmtm) REVERT: D 534 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8559 (mtpt) REVERT: D 579 LYS cc_start: 0.8818 (tmmt) cc_final: 0.8583 (ttpp) REVERT: D 624 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8484 (mmtm) REVERT: D 664 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7806 (tptm) REVERT: D 701 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8540 (mmtp) REVERT: E 318 VAL cc_start: 0.9049 (t) cc_final: 0.8836 (p) REVERT: E 325 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8569 (pp) REVERT: E 579 LYS cc_start: 0.8608 (tmtp) cc_final: 0.8372 (tmtt) REVERT: E 624 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8524 (mmtp) REVERT: E 647 ASP cc_start: 0.7937 (m-30) cc_final: 0.7694 (m-30) REVERT: F 300 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7083 (mt-10) REVERT: F 567 LEU cc_start: 0.8556 (tm) cc_final: 0.8322 (tt) REVERT: F 574 PHE cc_start: 0.5914 (m-10) cc_final: 0.5713 (m-10) REVERT: F 671 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8190 (mmm160) REVERT: F 695 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7685 (tm-30) REVERT: F 715 PHE cc_start: 0.8249 (t80) cc_final: 0.8037 (t80) REVERT: F 735 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7667 (mt-10) REVERT: G 530 LYS cc_start: 0.8517 (mttt) cc_final: 0.8294 (mptp) REVERT: G 673 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8537 (ttmm) REVERT: G 737 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7710 (t0) outliers start: 69 outliers final: 50 residues processed: 636 average time/residue: 1.2259 time to fit residues: 884.5993 Evaluate side-chains 665 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 608 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 562 LEU 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 560 ILE Chi-restraints excluded: chain B residue 563 LEU 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 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR 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 526 LYS Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 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 664 LYS 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 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 310 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 560 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 739 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 247 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 222 optimal weight: 0.0570 chunk 207 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS 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 648 GLN G 525 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 = 0.3878 r_free = 0.3878 target = 0.136679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108768 restraints weight = 33015.722| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.00 r_work: 0.3323 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3894 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= 0.138 Angle : 0.576 13.129 28424 Z= 0.289 Chirality : 0.042 0.278 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.010 58.706 2781 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 21.51 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.17), residues: 2540 helix: 2.99 (0.12), residues: 1614 sheet: 0.19 (0.27), residues: 341 loop : 0.23 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 548 HIS 0.005 0.001 HIS E 708 PHE 0.030 0.001 PHE G 301 TYR 0.011 0.001 TYR D 740 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 1505) hydrogen bonds : angle 3.91433 ( 4437) covalent geometry : bond 0.00313 (20974) covalent geometry : angle 0.57603 (28424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22133.57 seconds wall clock time: 378 minutes 7.51 seconds (22687.51 seconds total)