Starting phenix.real_space_refine on Sat Sep 28 23:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_24186.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_24186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_24186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_24186.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/09_2024/7n5d_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.64, per 1000 atoms: 0.61 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: 5.13 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: 2.10 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: 6.62 Time building geometry restraints manager: 6.01 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: 1.300 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: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 45.670 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.690 ------------------------------------------------------------------------------- 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= 1.464 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 2.346 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: 1.1815 time to fit residues: 1064.4849 Evaluate side-chains 646 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 640 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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= 0.233 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 *********************** 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 fitting. rotamer outliers: 82 poor density : 690 time to evaluate : 2.428 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 302 VAL cc_start: 0.8591 (t) cc_final: 0.8338 (m) REVERT: A 315 LEU cc_start: 0.8243 (mt) cc_final: 0.8020 (mt) REVERT: A 330 PHE cc_start: 0.7413 (t80) cc_final: 0.7098 (t80) REVERT: A 576 ASN cc_start: 0.7377 (t0) cc_final: 0.7073 (t0) REVERT: A 723 SER cc_start: 0.8239 (t) cc_final: 0.7989 (m) REVERT: B 324 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8093 (mmtt) REVERT: B 328 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8402 (t) REVERT: B 576 ASN cc_start: 0.7375 (m-40) cc_final: 0.7134 (m110) REVERT: B 583 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 686 GLN cc_start: 0.8030 (mp-120) cc_final: 0.7816 (mp10) REVERT: D 297 LYS cc_start: 0.7144 (tttt) cc_final: 0.6932 (mmpt) REVERT: D 307 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (m) REVERT: D 314 PHE cc_start: 0.7956 (t80) cc_final: 0.7734 (t80) REVERT: D 689 MET cc_start: 0.8358 (ttp) cc_final: 0.8158 (ttp) REVERT: F 671 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8230 (mmm-85) REVERT: F 677 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7406 (mt-10) REVERT: F 735 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7363 (mt-10) REVERT: G 715 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7484 (m-80) outliers start: 82 outliers final: 27 residues processed: 716 average time/residue: 1.1509 time to fit residues: 938.6847 Evaluate side-chains 683 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 653 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 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 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 131 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 686 GLN C 648 GLN C 698 ASN C 713 GLN D 291 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 525 ASN G 576 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20974 Z= 0.260 Angle : 0.553 8.091 28424 Z= 0.287 Chirality : 0.042 0.258 3452 Planarity : 0.003 0.040 3469 Dihedral : 6.868 58.345 2785 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.17 % Allowed : 16.74 % Favored : 79.09 % 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: 2.75 (0.16), residues: 2540 helix: 2.62 (0.12), residues: 1613 sheet: 0.54 (0.28), residues: 299 loop : 0.39 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 273 HIS 0.006 0.001 HIS A 592 PHE 0.026 0.002 PHE G 301 TYR 0.014 0.001 TYR E 740 ARG 0.007 0.001 ARG B 720 *********************** 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 744 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 654 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 311 ILE cc_start: 0.8747 (tp) cc_final: 0.8487 (tp) REVERT: A 737 ASP cc_start: 0.7823 (t0) cc_final: 0.7461 (t0) REVERT: B 583 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 686 GLN cc_start: 0.8074 (mp10) cc_final: 0.7870 (mp10) REVERT: C 299 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6705 (mm) REVERT: C 300 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7254 (mp0) REVERT: C 713 GLN cc_start: 0.8050 (tp40) cc_final: 0.7760 (tp40) REVERT: D 282 VAL cc_start: 0.7776 (p) cc_final: 0.7572 (m) REVERT: E 325 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8539 (pp) REVERT: F 548 TRP cc_start: 0.8290 (t60) cc_final: 0.7867 (t60) REVERT: F 671 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: F 735 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7432 (mt-10) REVERT: G 545 ILE cc_start: 0.8717 (mp) cc_final: 0.8494 (mp) REVERT: G 715 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7477 (m-80) outliers start: 90 outliers final: 46 residues processed: 682 average time/residue: 1.1827 time to fit residues: 919.0815 Evaluate side-chains 677 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 628 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 569 VAL Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 299 LEU 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 300 GLU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 ILE 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 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU 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 560 ILE Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 686 GLN B 576 ASN B 613 ASN C 576 ASN C 648 GLN D 576 ASN D 648 GLN E 688 ASN F 525 ASN F 576 ASN F 688 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20974 Z= 0.250 Angle : 0.546 13.504 28424 Z= 0.279 Chirality : 0.042 0.225 3452 Planarity : 0.003 0.037 3469 Dihedral : 6.673 57.874 2783 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.40 % Allowed : 18.22 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2540 helix: 2.71 (0.12), residues: 1613 sheet: 0.22 (0.27), residues: 341 loop : 0.35 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 548 HIS 0.006 0.001 HIS E 708 PHE 0.024 0.002 PHE D 301 TYR 0.010 0.001 TYR E 740 ARG 0.004 0.000 ARG B 644 *********************** 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 730 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 635 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7135 (pmt170) cc_final: 0.6904 (pmt170) REVERT: A 300 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 717 GLU cc_start: 0.6963 (tp30) cc_final: 0.6675 (tp30) REVERT: A 737 ASP cc_start: 0.7824 (t0) cc_final: 0.7437 (t0) REVERT: B 300 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6947 (mp0) REVERT: B 686 GLN cc_start: 0.8060 (mp10) cc_final: 0.7859 (mp10) REVERT: C 300 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7317 (mp0) REVERT: C 713 GLN cc_start: 0.8053 (tp40) cc_final: 0.7815 (tp40) REVERT: E 325 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8568 (pp) REVERT: F 548 TRP cc_start: 0.8294 (t60) cc_final: 0.8011 (t60) REVERT: F 671 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8271 (mmm160) REVERT: F 735 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7511 (mt-10) REVERT: G 545 ILE cc_start: 0.8692 (mp) cc_final: 0.8460 (mp) REVERT: G 715 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7547 (m-80) outliers start: 95 outliers final: 54 residues processed: 671 average time/residue: 1.1507 time to fit residues: 879.0786 Evaluate side-chains 686 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 630 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 576 ASN 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 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 C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 635 CYS 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 541 ILE 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 662 VAL Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 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 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 545 ILE Chi-restraints excluded: chain F residue 560 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 G residue 324 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 173 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 C 648 GLN D 531 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20974 Z= 0.184 Angle : 0.520 10.928 28424 Z= 0.265 Chirality : 0.041 0.282 3452 Planarity : 0.003 0.036 3469 Dihedral : 6.457 59.522 2783 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.76 % Allowed : 19.29 % Favored : 76.96 % 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: 2.85 (0.12), residues: 1613 sheet: 0.21 (0.27), residues: 341 loop : 0.28 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 548 HIS 0.004 0.001 HIS A 592 PHE 0.026 0.001 PHE G 301 TYR 0.008 0.001 TYR E 740 ARG 0.002 0.000 ARG A 671 *********************** 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 714 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 633 time to evaluate : 2.304 Fit side-chains REVERT: A 296 ARG cc_start: 0.7055 (pmt170) cc_final: 0.6794 (pmt170) REVERT: A 300 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 323 LEU cc_start: 0.8295 (mt) cc_final: 0.7967 (tm) REVERT: A 717 GLU cc_start: 0.6909 (tp30) cc_final: 0.6673 (tp30) REVERT: A 737 ASP cc_start: 0.7817 (t0) cc_final: 0.7398 (t0) REVERT: B 300 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6933 (mt-10) REVERT: B 629 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 689 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: C 300 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7325 (mp0) REVERT: E 300 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7524 (mp0) REVERT: E 325 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8571 (pp) REVERT: F 671 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8281 (mmm-85) REVERT: F 735 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7441 (mt-10) REVERT: G 545 ILE cc_start: 0.8678 (mp) cc_final: 0.8460 (mp) REVERT: G 715 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7426 (m-80) outliers start: 81 outliers final: 45 residues processed: 661 average time/residue: 1.2185 time to fit residues: 915.0045 Evaluate side-chains 680 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 631 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 670 ASP 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 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR 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 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 549 LEU 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 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 543 MET 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 G residue 697 VAL Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 C 648 GLN D 531 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20974 Z= 0.225 Angle : 0.533 9.643 28424 Z= 0.272 Chirality : 0.042 0.256 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.353 59.270 2781 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.03 % Allowed : 19.84 % 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: 2.91 (0.17), residues: 2540 helix: 2.88 (0.12), residues: 1613 sheet: 0.19 (0.26), residues: 341 loop : 0.28 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 548 HIS 0.005 0.001 HIS E 708 PHE 0.026 0.001 PHE F 574 TYR 0.012 0.001 TYR D 740 ARG 0.003 0.000 ARG D 296 *********************** 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 717 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 630 time to evaluate : 2.232 Fit side-chains REVERT: A 296 ARG cc_start: 0.7021 (pmt170) cc_final: 0.6765 (pmt170) REVERT: A 300 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 323 LEU cc_start: 0.8298 (mt) cc_final: 0.7988 (tm) REVERT: A 717 GLU cc_start: 0.6976 (tp30) cc_final: 0.6721 (tp30) REVERT: A 737 ASP cc_start: 0.7817 (t0) cc_final: 0.7455 (t0) REVERT: B 300 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6973 (mt-10) REVERT: B 301 PHE cc_start: 0.7352 (t80) cc_final: 0.7075 (t80) REVERT: B 629 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 689 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: C 300 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7365 (mp0) REVERT: C 713 GLN cc_start: 0.8030 (tp40) cc_final: 0.7689 (tp40) REVERT: D 548 TRP cc_start: 0.7562 (t60) cc_final: 0.7001 (t60) REVERT: E 300 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7573 (mp0) REVERT: E 325 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8576 (pp) REVERT: F 671 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8257 (mmm160) REVERT: F 735 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7478 (mt-10) REVERT: G 715 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7488 (m-80) outliers start: 87 outliers final: 50 residues processed: 657 average time/residue: 1.1365 time to fit residues: 849.6207 Evaluate side-chains 681 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 627 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 543 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 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 655 SER Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 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 545 ILE Chi-restraints excluded: chain D residue 547 ILE 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 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 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 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 211 optimal weight: 0.0980 chunk 140 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 C 648 GLN D 531 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20974 Z= 0.160 Angle : 0.527 10.495 28424 Z= 0.268 Chirality : 0.041 0.279 3452 Planarity : 0.003 0.034 3469 Dihedral : 6.207 57.595 2781 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.99 % Allowed : 20.12 % 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: 2.97 (0.17), residues: 2540 helix: 2.96 (0.12), residues: 1614 sheet: 0.14 (0.26), residues: 341 loop : 0.28 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 548 HIS 0.004 0.001 HIS E 708 PHE 0.032 0.001 PHE F 574 TYR 0.007 0.001 TYR D 740 ARG 0.005 0.000 ARG D 296 *********************** 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 720 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 634 time to evaluate : 2.174 Fit side-chains revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6605 (mp) REVERT: A 296 ARG cc_start: 0.6978 (pmt170) cc_final: 0.6750 (pmt170) REVERT: A 300 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 323 LEU cc_start: 0.8258 (mt) cc_final: 0.7930 (tm) REVERT: A 576 ASN cc_start: 0.7539 (t0) cc_final: 0.7233 (t0) REVERT: A 717 GLU cc_start: 0.6854 (tp30) cc_final: 0.6628 (tp30) REVERT: A 737 ASP cc_start: 0.7818 (t0) cc_final: 0.7415 (t0) REVERT: B 300 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 567 LEU cc_start: 0.8351 (tm) cc_final: 0.8114 (tt) REVERT: B 629 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7903 (t80) REVERT: B 689 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8032 (ttp) REVERT: C 300 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7397 (mp0) REVERT: D 664 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7667 (mttt) REVERT: E 300 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 325 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8573 (pp) REVERT: F 671 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: F 735 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7434 (mt-10) REVERT: G 715 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7378 (m-80) outliers start: 86 outliers final: 47 residues processed: 667 average time/residue: 1.1600 time to fit residues: 880.4571 Evaluate side-chains 671 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 618 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 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 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 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 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 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 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 697 VAL Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 0.0170 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 0.0040 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 196 optimal weight: 0.0980 overall best weight: 0.5632 ------------------------------------------------------------------------------- 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 576 ASN C 648 GLN C 713 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3819 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= 0.177 Angle : 0.542 10.776 28424 Z= 0.272 Chirality : 0.041 0.273 3452 Planarity : 0.003 0.033 3469 Dihedral : 6.115 58.837 2781 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.66 % Allowed : 21.00 % Favored : 75.34 % 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: 0.15 (0.27), residues: 341 loop : 0.27 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 548 HIS 0.004 0.001 HIS E 708 PHE 0.033 0.001 PHE F 574 TYR 0.009 0.001 TYR D 740 ARG 0.003 0.000 ARG A 334 *********************** 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 695 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 616 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6926 (pmt170) cc_final: 0.6702 (pmt170) REVERT: A 300 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 323 LEU cc_start: 0.8245 (mt) cc_final: 0.7936 (tm) REVERT: A 717 GLU cc_start: 0.6879 (tp30) cc_final: 0.6655 (tp30) REVERT: A 737 ASP cc_start: 0.7837 (t0) cc_final: 0.7403 (t0) REVERT: B 567 LEU cc_start: 0.8352 (tm) cc_final: 0.8148 (tt) REVERT: B 629 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7875 (t80) REVERT: B 689 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: C 300 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7382 (mp0) REVERT: D 664 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7673 (mttt) REVERT: E 300 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7532 (mt-10) REVERT: E 325 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8577 (pp) REVERT: F 671 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8267 (mmm160) REVERT: F 735 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7449 (mt-10) REVERT: G 715 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7400 (m-80) outliers start: 79 outliers final: 46 residues processed: 644 average time/residue: 1.1717 time to fit residues: 857.0395 Evaluate side-chains 662 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 611 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 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 324 LYS 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 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 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 560 ILE 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 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 543 MET 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 G residue 680 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 C 713 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3896 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= 0.178 Angle : 0.558 13.437 28424 Z= 0.278 Chirality : 0.041 0.188 3452 Planarity : 0.003 0.033 3469 Dihedral : 6.058 59.854 2781 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.25 % Allowed : 21.65 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.27), residues: 341 loop : 0.27 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 548 HIS 0.004 0.001 HIS E 708 PHE 0.027 0.001 PHE F 301 TYR 0.009 0.001 TYR D 740 ARG 0.003 0.000 ARG A 334 *********************** 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 679 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 609 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6909 (pmt170) cc_final: 0.6706 (pmt170) REVERT: A 300 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 323 LEU cc_start: 0.8236 (mt) cc_final: 0.7923 (tm) REVERT: A 717 GLU cc_start: 0.6858 (tp30) cc_final: 0.6632 (tp30) REVERT: A 737 ASP cc_start: 0.7808 (t0) cc_final: 0.7366 (t0) REVERT: B 301 PHE cc_start: 0.7327 (t80) cc_final: 0.7104 (t80) REVERT: B 567 LEU cc_start: 0.8326 (tm) cc_final: 0.8123 (tt) REVERT: B 629 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 689 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8041 (ttp) REVERT: C 300 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7409 (mp0) REVERT: C 689 MET cc_start: 0.8396 (ttp) cc_final: 0.8105 (ttp) REVERT: D 664 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7673 (mttt) REVERT: E 300 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7538 (mt-10) REVERT: E 325 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8594 (pp) REVERT: F 671 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8272 (mmm160) REVERT: F 735 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7436 (mt-10) REVERT: G 715 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7409 (m-80) outliers start: 70 outliers final: 47 residues processed: 635 average time/residue: 1.2500 time to fit residues: 909.0434 Evaluate side-chains 657 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 605 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 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 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 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 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 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 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 543 MET 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 G residue 680 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 C 713 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN G 698 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20974 Z= 0.276 Angle : 0.599 11.851 28424 Z= 0.300 Chirality : 0.043 0.217 3452 Planarity : 0.003 0.033 3469 Dihedral : 6.145 58.968 2781 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.01 % Allowed : 22.44 % Favored : 74.55 % 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: 2.92 (0.17), residues: 2540 helix: 2.90 (0.12), residues: 1614 sheet: 0.16 (0.26), residues: 341 loop : 0.27 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 273 HIS 0.006 0.001 HIS E 708 PHE 0.031 0.002 PHE A 330 TYR 0.013 0.002 TYR D 740 ARG 0.004 0.000 ARG A 296 ********************** 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 fitting. rotamer outliers: 65 poor density : 615 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7011 (pmt170) cc_final: 0.6775 (pmt170) REVERT: A 300 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 323 LEU cc_start: 0.8250 (mt) cc_final: 0.7950 (tm) REVERT: A 737 ASP cc_start: 0.7851 (t0) cc_final: 0.7407 (t0) REVERT: B 629 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 689 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: C 300 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7337 (mp0) REVERT: C 689 MET cc_start: 0.8431 (ttp) cc_final: 0.8182 (ttp) REVERT: E 300 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 325 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8599 (pp) REVERT: F 671 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8283 (mmm160) REVERT: F 735 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7481 (mt-10) REVERT: G 545 ILE cc_start: 0.8730 (mp) cc_final: 0.8439 (mp) REVERT: G 715 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (m-80) outliers start: 65 outliers final: 46 residues processed: 637 average time/residue: 1.2224 time to fit residues: 881.5589 Evaluate side-chains 663 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 613 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 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 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 324 LYS 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 629 TYR Chi-restraints excluded: chain C residue 635 CYS 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 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 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 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU 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 G residue 543 MET Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 715 PHE Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 C 713 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN ** G 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 = 0.3874 r_free = 0.3874 target = 0.137771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109351 restraints weight = 32718.325| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.03 r_work: 0.3320 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20974 Z= 0.234 Angle : 0.601 12.919 28424 Z= 0.300 Chirality : 0.042 0.197 3452 Planarity : 0.003 0.032 3469 Dihedral : 6.090 57.959 2781 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.97 % Allowed : 22.39 % Favored : 74.64 % 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: 2.91 (0.17), residues: 2540 helix: 2.90 (0.12), residues: 1614 sheet: 0.17 (0.27), residues: 341 loop : 0.22 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 548 HIS 0.006 0.001 HIS E 708 PHE 0.032 0.001 PHE G 301 TYR 0.012 0.001 TYR D 740 ARG 0.004 0.000 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11996.45 seconds wall clock time: 207 minutes 45.10 seconds (12465.10 seconds total)