Starting phenix.real_space_refine on Thu Jun 4 22:32:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x60_66603/06_2026/9x60_66603.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 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 78 5.16 5 C 9762 2.51 5 N 2670 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15618 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "P" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 778 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain breaks: 1 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "Q" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 778 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain breaks: 1 Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "R" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 778 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain breaks: 1 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.09, per 1000 atoms: 0.26 Number of scatterers: 15618 At special positions: 0 Unit cell: (140.27, 148.57, 156.04, 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 78 16.00 O 3108 8.00 N 2670 7.00 C 9762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.05 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.05 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.06 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 104 " distance=2.02 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=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 25 " " NAG A 402 " - " ASN A 59 " " NAG A 403 " - " ASN A 145 " " NAG A 404 " - " ASN A 167 " " NAG B 401 " - " ASN B 25 " " NAG B 402 " - " ASN B 59 " " NAG B 403 " - " ASN B 145 " " NAG B 404 " - " ASN B 167 " " NAG C 401 " - " ASN C 25 " " NAG C 402 " - " ASN C 59 " " NAG C 403 " - " ASN C 145 " " NAG C 404 " - " ASN C 167 " " NAG I 1 " - " ASN A 303 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN B 303 " " NAG M 1 " - " ASN B 332 " " NAG N 1 " - " ASN C 303 " " NAG O 1 " - " ASN C 332 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 761.9 milliseconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 14.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.679A pdb=" N VAL A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.587A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.512A pdb=" N TYR A 114 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 removed outlier: 4.163A pdb=" N LYS A 166 " --> pdb=" O ASP A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.690A pdb=" N LYS A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 385 through 391 Processing helix chain 'P' and resid 393 through 401 removed outlier: 3.579A pdb=" N ASN P 397 " --> pdb=" O LYS P 393 " (cutoff:3.500A) Processing helix chain 'P' and resid 420 through 452 removed outlier: 3.913A pdb=" N LEU P 426 " --> pdb=" O GLU P 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER P 440 " --> pdb=" O ASP P 436 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU P 443 " --> pdb=" O SER P 439 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU P 447 " --> pdb=" O GLU P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 464 removed outlier: 3.653A pdb=" N LEU P 464 " --> pdb=" O LEU P 461 " (cutoff:3.500A) Processing helix chain 'P' and resid 491 through 493 No H-bonds generated for 'chain 'P' and resid 491 through 493' Processing helix chain 'P' and resid 494 through 499 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.678A pdb=" N VAL B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.587A pdb=" N GLN B 106 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.511A pdb=" N TYR B 114 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 removed outlier: 4.163A pdb=" N LYS B 166 " --> pdb=" O ASP B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.690A pdb=" N LYS B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 391 Processing helix chain 'Q' and resid 393 through 401 removed outlier: 3.579A pdb=" N ASN Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) Processing helix chain 'Q' and resid 420 through 452 removed outlier: 3.913A pdb=" N LEU Q 426 " --> pdb=" O GLU Q 422 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER Q 440 " --> pdb=" O ASP Q 436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU Q 443 " --> pdb=" O SER Q 439 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 464 removed outlier: 3.653A pdb=" N LEU Q 464 " --> pdb=" O LEU Q 461 " (cutoff:3.500A) Processing helix chain 'Q' and resid 491 through 493 No H-bonds generated for 'chain 'Q' and resid 491 through 493' Processing helix chain 'Q' and resid 494 through 499 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.679A pdb=" N VAL C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.587A pdb=" N GLN C 106 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 3.511A pdb=" N TYR C 114 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 166 removed outlier: 4.163A pdb=" N LYS C 166 " --> pdb=" O ASP C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.691A pdb=" N LYS C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 391 Processing helix chain 'R' and resid 393 through 401 removed outlier: 3.579A pdb=" N ASN R 397 " --> pdb=" O LYS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 420 through 452 removed outlier: 3.912A pdb=" N LEU R 426 " --> pdb=" O GLU R 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 440 " --> pdb=" O ASP R 436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU R 443 " --> pdb=" O SER R 439 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU R 447 " --> pdb=" O GLU R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 464 removed outlier: 3.653A pdb=" N LEU R 464 " --> pdb=" O LEU R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 493 No H-bonds generated for 'chain 'R' and resid 491 through 493' Processing helix chain 'R' and resid 494 through 499 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.755A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.755A pdb=" N THR D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.755A pdb=" N THR F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 4.071A pdb=" N HIS A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.685A pdb=" N THR A 34 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.930A pdb=" N ASN A 43 " --> pdb=" O ALA A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.599A pdb=" N ILE A 282 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.554A pdb=" N VAL A 189 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A 266 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA9, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 17 removed outlier: 4.072A pdb=" N HIS B 14 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.684A pdb=" N THR B 34 " --> pdb=" O TYR B 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 44 removed outlier: 5.929A pdb=" N ASN B 43 " --> pdb=" O ALA B 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.599A pdb=" N ILE B 282 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 119 removed outlier: 7.553A pdb=" N VAL B 189 " --> pdb=" O PRO B 269 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 266 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP B 158 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AB8, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AB9, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 17 removed outlier: 4.071A pdb=" N HIS C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AC3, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.684A pdb=" N THR C 34 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 removed outlier: 5.929A pdb=" N ASN C 43 " --> pdb=" O ALA C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.598A pdb=" N ILE C 282 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.553A pdb=" N VAL C 189 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL C 266 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AC8, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AC9, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS H 104 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP H 118 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.557A pdb=" N ARG L 11 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU L 39 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 20 through 23 removed outlier: 4.034A pdb=" N GLU L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER L 83 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'D' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS D 104 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP D 118 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG D 106 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.556A pdb=" N ARG E 11 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 39 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 20 through 23 removed outlier: 4.034A pdb=" N GLU E 86 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER E 83 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG F 43 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS F 104 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP F 118 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG F 106 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.101A pdb=" N TRP F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG F 43 " --> pdb=" O TRP F 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.557A pdb=" N ARG G 11 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 39 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP G 41 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 20 through 23 removed outlier: 4.033A pdb=" N GLU G 86 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 83 " --> pdb=" O GLU G 86 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1209 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: 2.97 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5007 1.34 - 1.46: 3666 1.46 - 1.59: 7128 1.59 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 15912 Sorted by residual: bond pdb=" N VAL E 91 " pdb=" CA VAL E 91 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.32e-02 5.74e+03 9.34e+00 bond pdb=" N VAL G 91 " pdb=" CA VAL G 91 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.85e+00 bond pdb=" N VAL L 91 " pdb=" CA VAL L 91 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.35e-02 5.49e+03 8.64e+00 bond pdb=" CG LEU C 203 " pdb=" CD2 LEU C 203 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" CG LEU B 203 " pdb=" CD2 LEU B 203 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.85e+00 ... (remaining 15907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 21304 3.83 - 7.67: 251 7.67 - 11.50: 33 11.50 - 15.33: 0 15.33 - 19.16: 3 Bond angle restraints: 21591 Sorted by residual: angle pdb=" CB MET D 111C" pdb=" CG MET D 111C" pdb=" SD MET D 111C" ideal model delta sigma weight residual 112.70 131.86 -19.16 3.00e+00 1.11e-01 4.08e+01 angle pdb=" CB MET H 111C" pdb=" CG MET H 111C" pdb=" SD MET H 111C" ideal model delta sigma weight residual 112.70 131.86 -19.16 3.00e+00 1.11e-01 4.08e+01 angle pdb=" CB MET F 111C" pdb=" CG MET F 111C" pdb=" SD MET F 111C" ideal model delta sigma weight residual 112.70 131.83 -19.13 3.00e+00 1.11e-01 4.06e+01 angle pdb=" C ALA H 111B" pdb=" N MET H 111C" pdb=" CA MET H 111C" ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C ALA F 111B" pdb=" N MET F 111C" pdb=" CA MET F 111C" ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 ... (remaining 21586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8827 17.85 - 35.70: 867 35.70 - 53.56: 201 53.56 - 71.41: 26 71.41 - 89.26: 18 Dihedral angle restraints: 9939 sinusoidal: 4230 harmonic: 5709 Sorted by residual: dihedral pdb=" CB CYS A 294 " pdb=" SG CYS A 294 " pdb=" SG CYS A 320 " pdb=" CB CYS A 320 " ideal model delta sinusoidal sigma weight residual 93.00 20.42 72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B 294 " pdb=" SG CYS B 294 " pdb=" SG CYS B 320 " pdb=" CB CYS B 320 " ideal model delta sinusoidal sigma weight residual 93.00 20.47 72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS C 294 " pdb=" SG CYS C 294 " pdb=" SG CYS C 320 " pdb=" CB CYS C 320 " ideal model delta sinusoidal sigma weight residual 93.00 20.49 72.51 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 9936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2267 0.098 - 0.196: 237 0.196 - 0.293: 16 0.293 - 0.391: 3 0.391 - 0.489: 3 Chirality restraints: 2526 Sorted by residual: chirality pdb=" CB THR H 123 " pdb=" CA THR H 123 " pdb=" OG1 THR H 123 " pdb=" CG2 THR H 123 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB THR D 123 " pdb=" CA THR D 123 " pdb=" OG1 THR D 123 " pdb=" CG2 THR D 123 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CB THR F 123 " pdb=" CA THR F 123 " pdb=" OG1 THR F 123 " pdb=" CG2 THR F 123 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.88e+00 ... (remaining 2523 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 89 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C LEU L 89 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU L 89 " -0.020 2.00e-02 2.50e+03 pdb=" N THR L 90 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 234 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C THR B 234 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 234 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU B 235 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 234 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C THR A 234 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 234 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A 235 " -0.016 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 274 2.64 - 3.21: 12774 3.21 - 3.77: 23139 3.77 - 4.34: 32378 4.34 - 4.90: 55977 Nonbonded interactions: 124542 Sorted by model distance: nonbonded pdb=" CD1 ILE F 112A" pdb=" NH1 ARG G 108 " model vdw 2.079 3.540 nonbonded pdb=" NH1 ARG L 24 " pdb=" OE1 GLU L 86 " model vdw 2.190 3.120 nonbonded pdb=" NH1 ARG E 24 " pdb=" OE1 GLU E 86 " model vdw 2.191 3.120 nonbonded pdb=" NH1 ARG G 24 " pdb=" OE1 GLU G 86 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR C 178 " pdb=" O GLU C 184 " model vdw 2.264 3.040 ... (remaining 124537 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.490 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.010 0.093 15957 Z= 0.425 Angle : 1.115 19.164 21699 Z= 0.592 Chirality : 0.065 0.489 2526 Planarity : 0.008 0.069 2757 Dihedral : 15.115 89.262 6237 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.50 % Favored : 92.05 % Rotamer: Outliers : 1.72 % Allowed : 9.65 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.15), residues: 1974 helix: -3.69 (0.19), residues: 273 sheet: -1.70 (0.23), residues: 468 loop : -3.36 (0.13), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 37 TYR 0.018 0.003 TYR H 103 PHE 0.027 0.003 PHE C 192 TRP 0.019 0.004 TRP F 52 HIS 0.009 0.003 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.43 (15912) covalent geometry : angle 1.10744 / 0.59 (21591) SS BOND : bond 0.01067 / 0.77 ( 18) SS BOND : angle 2.38892 / 1.46 ( 36) hydrogen bonds : bond 0.14709 / 10.33 ( 425) hydrogen bonds : angle 7.37197 / 5.03 ( 1209) Misc. bond : bond 0.00055 / 0.03 ( 3) link_BETA1-4 : bond 0.00366 / 0.25 ( 6) link_BETA1-4 : angle 2.38954 / 1.49 ( 18) link_NAG-ASN : bond 0.00999 / 0.69 ( 18) link_NAG-ASN : angle 1.93768 / 1.31 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7334 (tttp) cc_final: 0.6593 (pttm) REVERT: A 52 LYS cc_start: 0.7744 (mttt) cc_final: 0.7513 (mtmm) REVERT: A 129 LYS cc_start: 0.8550 (mttt) cc_final: 0.8327 (mtpp) REVERT: A 304 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7820 (tttp) REVERT: P 399 ASN cc_start: 0.7923 (m-40) cc_final: 0.7720 (m-40) REVERT: B 52 LYS cc_start: 0.7772 (mttt) cc_final: 0.7548 (mtmm) REVERT: B 129 LYS cc_start: 0.8592 (mttt) cc_final: 0.8369 (mtpp) REVERT: B 278 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8169 (ttm-80) REVERT: B 304 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: B 312 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7294 (mt-10) REVERT: C 278 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8283 (ttm110) REVERT: R 399 ASN cc_start: 0.8071 (m-40) cc_final: 0.7851 (m-40) REVERT: D 90 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: F 40 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8303 (m) REVERT: F 67 TYR cc_start: 0.8509 (m-80) cc_final: 0.8067 (m-80) REVERT: G 38 TYR cc_start: 0.8715 (m-80) cc_final: 0.8470 (m-80) outliers start: 29 outliers final: 4 residues processed: 271 average time/residue: 0.1219 time to fit residues: 49.6925 Evaluate side-chains 191 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 397 ASN P 441 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 392 ASN Q 397 ASN Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN R 397 ASN R 441 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109724 restraints weight = 17477.158| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.69 r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15957 Z= 0.140 Angle : 0.633 8.349 21699 Z= 0.328 Chirality : 0.045 0.197 2526 Planarity : 0.005 0.051 2757 Dihedral : 7.308 59.959 2668 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 2.49 % Allowed : 13.03 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.16), residues: 1974 helix: -2.49 (0.27), residues: 279 sheet: -1.42 (0.23), residues: 489 loop : -2.90 (0.15), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 434 TYR 0.012 0.001 TYR F 103 PHE 0.014 0.001 PHE A 192 TRP 0.013 0.001 TRP F 52 HIS 0.005 0.001 HIS G 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (15912) covalent geometry : angle 0.62549 / 0.33 (21591) SS BOND : bond 0.00626 / 0.34 ( 18) SS BOND : angle 1.68771 / 1.04 ( 36) hydrogen bonds : bond 0.03292 / 2.28 ( 425) hydrogen bonds : angle 5.49487 / 3.76 ( 1209) Misc. bond : bond 0.00060 / 0.03 ( 3) link_BETA1-4 : bond 0.00225 / 0.15 ( 6) link_BETA1-4 : angle 1.60530 / 1.04 ( 18) link_NAG-ASN : bond 0.00267 / 0.19 ( 18) link_NAG-ASN : angle 1.36791 / 0.94 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7032 (tttp) cc_final: 0.6067 (pttm) REVERT: A 52 LYS cc_start: 0.7521 (mttt) cc_final: 0.7051 (mtmm) REVERT: A 105 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.7808 (mtt-85) REVERT: A 129 LYS cc_start: 0.8486 (mttt) cc_final: 0.8018 (mtpp) REVERT: A 304 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6766 (tttp) REVERT: P 399 ASN cc_start: 0.7174 (m-40) cc_final: 0.6970 (m-40) REVERT: B 52 LYS cc_start: 0.7562 (mttt) cc_final: 0.7094 (mtmm) REVERT: B 129 LYS cc_start: 0.8509 (mttt) cc_final: 0.8045 (mtpp) REVERT: B 304 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6773 (tttp) REVERT: B 312 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7881 (mt-10) REVERT: Q 388 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7466 (mm110) REVERT: Q 447 LEU cc_start: 0.7047 (mp) cc_final: 0.6835 (tt) REVERT: C 17 LYS cc_start: 0.6950 (tttp) cc_final: 0.5908 (pttm) REVERT: C 40 TYR cc_start: 0.8428 (p90) cc_final: 0.8195 (p90) REVERT: C 48 ARG cc_start: 0.6621 (ptm160) cc_final: 0.6214 (ptm160) REVERT: C 150 ILE cc_start: 0.7411 (mt) cc_final: 0.7089 (tp) REVERT: R 388 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7354 (mm110) REVERT: R 399 ASN cc_start: 0.7348 (m-40) cc_final: 0.7144 (m-40) REVERT: D 90 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: D 111 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8011 (mmt) REVERT: F 67 TYR cc_start: 0.8037 (m-80) cc_final: 0.7281 (m-80) REVERT: F 111 MET cc_start: 0.8155 (mmp) cc_final: 0.7888 (mmp) outliers start: 42 outliers final: 28 residues processed: 213 average time/residue: 0.1179 time to fit residues: 38.2815 Evaluate side-chains 204 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 436 ASP Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain R residue 455 ASN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 113 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 134 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 460 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 441 GLN L 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109488 restraints weight = 17645.115| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.66 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15957 Z= 0.148 Angle : 0.590 8.931 21699 Z= 0.303 Chirality : 0.044 0.164 2526 Planarity : 0.005 0.045 2757 Dihedral : 6.353 59.249 2665 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 3.26 % Allowed : 14.21 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.17), residues: 1974 helix: -1.84 (0.29), residues: 276 sheet: -1.05 (0.24), residues: 471 loop : -2.67 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 244 TYR 0.013 0.001 TYR D 103 PHE 0.014 0.002 PHE B 192 TRP 0.012 0.002 TRP D 52 HIS 0.005 0.001 HIS P 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (15912) covalent geometry : angle 0.58291 / 0.30 (21591) SS BOND : bond 0.00444 / 0.31 ( 18) SS BOND : angle 1.67962 / 1.03 ( 36) hydrogen bonds : bond 0.02958 / 2.06 ( 425) hydrogen bonds : angle 5.01392 / 3.42 ( 1209) Misc. bond : bond 0.00048 / 0.03 ( 3) link_BETA1-4 : bond 0.00321 / 0.19 ( 6) link_BETA1-4 : angle 1.42508 / 0.92 ( 18) link_NAG-ASN : bond 0.00244 / 0.17 ( 18) link_NAG-ASN : angle 1.15577 / 0.77 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7141 (tttp) cc_final: 0.6264 (pttt) REVERT: A 52 LYS cc_start: 0.7688 (mttt) cc_final: 0.7265 (mtmm) REVERT: A 105 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: A 304 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7024 (tttp) REVERT: P 436 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 17 LYS cc_start: 0.6865 (tttp) cc_final: 0.5989 (pttm) REVERT: B 52 LYS cc_start: 0.7713 (mttt) cc_final: 0.7213 (mtmm) REVERT: B 129 LYS cc_start: 0.8542 (mttt) cc_final: 0.8080 (mtpp) REVERT: B 304 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6887 (tttp) REVERT: Q 436 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7002 (t0) REVERT: C 17 LYS cc_start: 0.7006 (tttp) cc_final: 0.5943 (pttt) REVERT: C 40 TYR cc_start: 0.8457 (p90) cc_final: 0.8251 (p90) REVERT: C 52 LYS cc_start: 0.7660 (mttt) cc_final: 0.7146 (mtmm) REVERT: D 90 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: F 23 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (t) REVERT: F 67 TYR cc_start: 0.8083 (m-80) cc_final: 0.7300 (m-80) outliers start: 55 outliers final: 37 residues processed: 221 average time/residue: 0.1144 time to fit residues: 38.7359 Evaluate side-chains 215 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 436 ASP Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain Q residue 462 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain R residue 455 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 388 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113593 restraints weight = 18018.119| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.65 r_work: 0.3143 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15957 Z= 0.121 Angle : 0.555 8.460 21699 Z= 0.284 Chirality : 0.043 0.153 2526 Planarity : 0.004 0.046 2757 Dihedral : 5.687 58.043 2664 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.14 % Allowed : 15.45 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.17), residues: 1974 helix: -1.42 (0.31), residues: 276 sheet: -0.83 (0.25), residues: 471 loop : -2.46 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 75 TYR 0.016 0.001 TYR L 38 PHE 0.013 0.001 PHE A 192 TRP 0.011 0.001 TRP F 52 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (15912) covalent geometry : angle 0.54934 / 0.28 (21591) SS BOND : bond 0.00407 / 0.28 ( 18) SS BOND : angle 1.57055 / 0.97 ( 36) hydrogen bonds : bond 0.02629 / 1.82 ( 425) hydrogen bonds : angle 4.75370 / 3.25 ( 1209) Misc. bond : bond 0.00042 / 0.02 ( 3) link_BETA1-4 : bond 0.00302 / 0.21 ( 6) link_BETA1-4 : angle 1.26506 / 0.82 ( 18) link_NAG-ASN : bond 0.00201 / 0.14 ( 18) link_NAG-ASN : angle 0.98368 / 0.65 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7146 (tttp) cc_final: 0.6205 (pttm) REVERT: A 52 LYS cc_start: 0.7776 (mttt) cc_final: 0.7348 (mtmm) REVERT: A 105 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7946 (mtt-85) REVERT: P 436 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 17 LYS cc_start: 0.6894 (tttp) cc_final: 0.6003 (pttm) REVERT: B 52 LYS cc_start: 0.7797 (mttt) cc_final: 0.7296 (mtmm) REVERT: Q 388 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7205 (mm110) REVERT: Q 436 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7147 (t0) REVERT: C 17 LYS cc_start: 0.7146 (tttp) cc_final: 0.6192 (pttt) REVERT: C 52 LYS cc_start: 0.7786 (mttt) cc_final: 0.7293 (mtmm) REVERT: C 232 ASP cc_start: 0.7335 (m-30) cc_final: 0.7070 (m-30) REVERT: H 40 SER cc_start: 0.8239 (m) cc_final: 0.7868 (t) REVERT: D 90 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: F 23 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7710 (t) REVERT: F 67 TYR cc_start: 0.8124 (m-80) cc_final: 0.7323 (m-80) REVERT: G 125 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6336 (mm-30) outliers start: 53 outliers final: 41 residues processed: 232 average time/residue: 0.1055 time to fit residues: 38.7164 Evaluate side-chains 226 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain P residue 436 ASP Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain R residue 455 ASN Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 441 GLN B 85 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN E 6 GLN E 114 ASN F 113 ASN G 6 GLN G 114 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105322 restraints weight = 18271.096| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.60 r_work: 0.3021 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 15957 Z= 0.362 Angle : 0.759 8.114 21699 Z= 0.382 Chirality : 0.050 0.193 2526 Planarity : 0.005 0.052 2757 Dihedral : 6.270 56.047 2655 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.35 % Favored : 92.50 % Rotamer: Outliers : 3.43 % Allowed : 17.17 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.17), residues: 1974 helix: -1.74 (0.29), residues: 279 sheet: -0.88 (0.26), residues: 444 loop : -2.59 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 434 TYR 0.014 0.002 TYR A 262 PHE 0.024 0.002 PHE C 192 TRP 0.021 0.003 TRP H 52 HIS 0.008 0.002 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.36 (15912) covalent geometry : angle 0.74701 / 0.38 (21591) SS BOND : bond 0.00722 / 0.49 ( 18) SS BOND : angle 2.69371 / 1.64 ( 36) hydrogen bonds : bond 0.03825 / 2.67 ( 425) hydrogen bonds : angle 5.14836 / 3.49 ( 1209) Misc. bond : bond 0.00089 / 0.05 ( 3) link_BETA1-4 : bond 0.00143 / 0.10 ( 6) link_BETA1-4 : angle 1.86694 / 1.20 ( 18) link_NAG-ASN : bond 0.00482 / 0.34 ( 18) link_NAG-ASN : angle 1.44912 / 0.95 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7068 (tttp) cc_final: 0.6176 (pttm) REVERT: A 38 LYS cc_start: 0.7885 (tptm) cc_final: 0.7681 (tptt) REVERT: A 52 LYS cc_start: 0.7882 (mttt) cc_final: 0.7420 (mtmm) REVERT: A 304 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7453 (tttp) REVERT: P 405 GLU cc_start: 0.8335 (pt0) cc_final: 0.7822 (pm20) REVERT: B 17 LYS cc_start: 0.6916 (tttp) cc_final: 0.6141 (pttm) REVERT: B 52 LYS cc_start: 0.7896 (mttt) cc_final: 0.7434 (mtmm) REVERT: B 129 LYS cc_start: 0.8623 (mttt) cc_final: 0.8177 (mtpp) REVERT: B 304 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7285 (tttp) REVERT: B 312 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7839 (mt-10) REVERT: Q 436 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7364 (t0) REVERT: C 17 LYS cc_start: 0.7253 (tttp) cc_final: 0.6173 (pttt) REVERT: C 52 LYS cc_start: 0.7929 (mttt) cc_final: 0.7463 (mtmm) REVERT: H 77 THR cc_start: 0.7874 (p) cc_final: 0.7623 (t) REVERT: L 125 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6513 (mm-30) REVERT: F 23 CYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7724 (t) REVERT: F 67 TYR cc_start: 0.8246 (m-80) cc_final: 0.7448 (m-80) REVERT: F 111 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7904 (mmt) outliers start: 58 outliers final: 44 residues processed: 221 average time/residue: 0.1081 time to fit residues: 37.3508 Evaluate side-chains 216 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain Q residue 462 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain G residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 127 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 441 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109954 restraints weight = 17983.060| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.72 r_work: 0.3101 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15957 Z= 0.135 Angle : 0.569 8.749 21699 Z= 0.291 Chirality : 0.043 0.155 2526 Planarity : 0.004 0.047 2757 Dihedral : 5.427 34.865 2652 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 2.84 % Allowed : 18.65 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 1974 helix: -1.24 (0.31), residues: 279 sheet: -0.74 (0.26), residues: 447 loop : -2.31 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.016 0.001 TYR E 38 PHE 0.013 0.001 PHE A 192 TRP 0.016 0.002 TRP H 52 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (15912) covalent geometry : angle 0.56267 / 0.29 (21591) SS BOND : bond 0.00423 / 0.29 ( 18) SS BOND : angle 1.74128 / 1.07 ( 36) hydrogen bonds : bond 0.02769 / 1.91 ( 425) hydrogen bonds : angle 4.75050 / 3.24 ( 1209) Misc. bond : bond 0.00054 / 0.03 ( 3) link_BETA1-4 : bond 0.00327 / 0.23 ( 6) link_BETA1-4 : angle 1.32413 / 0.85 ( 18) link_NAG-ASN : bond 0.00201 / 0.14 ( 18) link_NAG-ASN : angle 0.93909 / 0.62 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7134 (tttp) cc_final: 0.6210 (pttm) REVERT: A 52 LYS cc_start: 0.7801 (mttt) cc_final: 0.7318 (mtmm) REVERT: A 105 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.7959 (mtt-85) REVERT: A 304 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7285 (tttp) REVERT: P 405 GLU cc_start: 0.8299 (pt0) cc_final: 0.7736 (pm20) REVERT: B 17 LYS cc_start: 0.6880 (tttp) cc_final: 0.6092 (pttm) REVERT: B 52 LYS cc_start: 0.7817 (mttt) cc_final: 0.7281 (mtmm) REVERT: B 129 LYS cc_start: 0.8570 (mttt) cc_final: 0.8120 (mtpp) REVERT: B 312 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7779 (mt-10) REVERT: Q 436 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7138 (t0) REVERT: C 17 LYS cc_start: 0.7187 (tttp) cc_final: 0.6078 (pttt) REVERT: C 52 LYS cc_start: 0.7826 (mttt) cc_final: 0.7364 (mtmm) REVERT: L 125 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6465 (mm-30) REVERT: E 103 TYR cc_start: 0.8174 (m-80) cc_final: 0.7899 (m-80) REVERT: F 23 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7742 (t) REVERT: F 67 TYR cc_start: 0.8093 (m-80) cc_final: 0.7298 (m-80) outliers start: 48 outliers final: 36 residues processed: 217 average time/residue: 0.1146 time to fit residues: 39.3999 Evaluate side-chains 213 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 388 GLN ** P 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112190 restraints weight = 17916.455| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.68 r_work: 0.3129 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15957 Z= 0.110 Angle : 0.537 8.497 21699 Z= 0.272 Chirality : 0.042 0.198 2526 Planarity : 0.004 0.046 2757 Dihedral : 4.897 34.067 2652 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.08 % Allowed : 19.54 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.18), residues: 1974 helix: -0.80 (0.32), residues: 279 sheet: -0.62 (0.26), residues: 450 loop : -2.10 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.012 0.001 TYR H 103 PHE 0.012 0.001 PHE A 192 TRP 0.011 0.001 TRP D 52 HIS 0.004 0.001 HIS L 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15912) covalent geometry : angle 0.53118 / 0.27 (21591) SS BOND : bond 0.00373 / 0.26 ( 18) SS BOND : angle 1.54763 / 0.95 ( 36) hydrogen bonds : bond 0.02484 / 1.71 ( 425) hydrogen bonds : angle 4.47742 / 3.06 ( 1209) Misc. bond : bond 0.00045 / 0.03 ( 3) link_BETA1-4 : bond 0.00291 / 0.21 ( 6) link_BETA1-4 : angle 1.22899 / 0.80 ( 18) link_NAG-ASN : bond 0.00184 / 0.13 ( 18) link_NAG-ASN : angle 0.89422 / 0.59 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6998 (tttp) cc_final: 0.6133 (pttm) REVERT: A 52 LYS cc_start: 0.7788 (mttt) cc_final: 0.7359 (mtmm) REVERT: A 105 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7850 (mtt-85) REVERT: A 304 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7186 (tttp) REVERT: P 405 GLU cc_start: 0.8260 (pt0) cc_final: 0.7716 (pm20) REVERT: B 17 LYS cc_start: 0.6877 (tttp) cc_final: 0.6072 (pttm) REVERT: B 52 LYS cc_start: 0.7909 (mttt) cc_final: 0.7354 (mtmm) REVERT: B 71 MET cc_start: 0.7593 (mtm) cc_final: 0.7312 (mtm) REVERT: B 312 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7792 (mt-10) REVERT: Q 436 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7042 (t0) REVERT: C 17 LYS cc_start: 0.7040 (tttp) cc_final: 0.6115 (pttt) REVERT: C 52 LYS cc_start: 0.7859 (mttt) cc_final: 0.7372 (mtmm) REVERT: C 90 VAL cc_start: 0.6630 (OUTLIER) cc_final: 0.6303 (m) REVERT: C 232 ASP cc_start: 0.7247 (m-30) cc_final: 0.7042 (m-30) REVERT: L 125 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: E 103 TYR cc_start: 0.7994 (m-80) cc_final: 0.7785 (m-80) REVERT: F 67 TYR cc_start: 0.8053 (m-80) cc_final: 0.7222 (m-80) REVERT: G 125 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6116 (mm-30) outliers start: 52 outliers final: 36 residues processed: 230 average time/residue: 0.1007 time to fit residues: 36.4085 Evaluate side-chains 222 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 439 SER Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain Q residue 436 ASP Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain Q residue 455 ASN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain R residue 439 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 55 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 185 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 160 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.1732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111231 restraints weight = 18051.975| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.69 r_work: 0.3177 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15957 Z= 0.086 Angle : 0.506 8.584 21699 Z= 0.257 Chirality : 0.042 0.154 2526 Planarity : 0.004 0.048 2757 Dihedral : 4.443 32.882 2652 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.25 % Allowed : 20.31 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.18), residues: 1974 helix: -0.42 (0.33), residues: 270 sheet: -0.43 (0.24), residues: 501 loop : -1.93 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 244 TYR 0.011 0.001 TYR D 103 PHE 0.008 0.001 PHE B 192 TRP 0.013 0.001 TRP C 158 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (15912) covalent geometry : angle 0.50295 / 0.26 (21591) SS BOND : bond 0.00273 / 0.19 ( 18) SS BOND : angle 1.19145 / 0.74 ( 36) hydrogen bonds : bond 0.02216 / 1.51 ( 425) hydrogen bonds : angle 4.30095 / 2.95 ( 1209) Misc. bond : bond 0.00036 / 0.02 ( 3) link_BETA1-4 : bond 0.00268 / 0.18 ( 6) link_BETA1-4 : angle 1.03939 / 0.65 ( 18) link_NAG-ASN : bond 0.00221 / 0.15 ( 18) link_NAG-ASN : angle 0.77741 / 0.52 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7035 (tttp) cc_final: 0.6185 (pttm) REVERT: A 52 LYS cc_start: 0.7878 (mttt) cc_final: 0.7444 (mtmm) REVERT: A 90 VAL cc_start: 0.6265 (OUTLIER) cc_final: 0.5833 (m) REVERT: A 105 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7869 (mtt-85) REVERT: A 304 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7271 (tttp) REVERT: P 405 GLU cc_start: 0.8231 (pt0) cc_final: 0.7656 (pm20) REVERT: B 17 LYS cc_start: 0.6946 (tttp) cc_final: 0.6180 (pttm) REVERT: B 52 LYS cc_start: 0.8020 (mttt) cc_final: 0.7470 (mtmm) REVERT: B 128 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 312 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7780 (mt-10) REVERT: Q 436 ASP cc_start: 0.7323 (m-30) cc_final: 0.7111 (t0) REVERT: C 17 LYS cc_start: 0.7193 (tttp) cc_final: 0.6231 (pttt) REVERT: C 52 LYS cc_start: 0.7959 (mttt) cc_final: 0.7492 (mtmm) REVERT: C 90 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6280 (m) REVERT: C 198 ASN cc_start: 0.8078 (m-40) cc_final: 0.7699 (t0) REVERT: C 235 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: R 405 GLU cc_start: 0.8289 (pt0) cc_final: 0.7731 (pm20) REVERT: E 39 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7117 (tp) REVERT: F 67 TYR cc_start: 0.8087 (m-80) cc_final: 0.7374 (m-80) REVERT: G 125 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6060 (mm-30) outliers start: 38 outliers final: 19 residues processed: 214 average time/residue: 0.1077 time to fit residues: 36.1233 Evaluate side-chains 205 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 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 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 441 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN R 441 GLN E 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112002 restraints weight = 18070.667| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.71 r_work: 0.3123 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15957 Z= 0.143 Angle : 0.547 8.632 21699 Z= 0.275 Chirality : 0.043 0.147 2526 Planarity : 0.004 0.047 2757 Dihedral : 4.632 33.047 2652 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.49 % Allowed : 20.31 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.18), residues: 1974 helix: -0.38 (0.32), residues: 279 sheet: -0.53 (0.24), residues: 519 loop : -1.90 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.012 0.001 TYR D 103 PHE 0.015 0.001 PHE C 192 TRP 0.016 0.002 TRP C 158 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (15912) covalent geometry : angle 0.53988 / 0.27 (21591) SS BOND : bond 0.00474 / 0.33 ( 18) SS BOND : angle 1.78671 / 1.10 ( 36) hydrogen bonds : bond 0.02555 / 1.76 ( 425) hydrogen bonds : angle 4.35561 / 2.98 ( 1209) Misc. bond : bond 0.00042 / 0.02 ( 3) link_BETA1-4 : bond 0.00277 / 0.19 ( 6) link_BETA1-4 : angle 1.26174 / 0.81 ( 18) link_NAG-ASN : bond 0.00195 / 0.13 ( 18) link_NAG-ASN : angle 0.92147 / 0.61 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6963 (tttp) cc_final: 0.6054 (pttm) REVERT: A 52 LYS cc_start: 0.7867 (mttt) cc_final: 0.7423 (mtmm) REVERT: A 304 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7237 (tttp) REVERT: P 405 GLU cc_start: 0.8227 (pt0) cc_final: 0.7654 (pm20) REVERT: B 17 LYS cc_start: 0.6909 (tttp) cc_final: 0.6150 (pttm) REVERT: B 52 LYS cc_start: 0.7905 (mttt) cc_final: 0.7393 (mtmm) REVERT: B 128 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 129 LYS cc_start: 0.8515 (mttt) cc_final: 0.8083 (mtpp) REVERT: B 312 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7775 (mt-10) REVERT: Q 436 ASP cc_start: 0.7330 (m-30) cc_final: 0.7070 (t0) REVERT: C 17 LYS cc_start: 0.7049 (tttp) cc_final: 0.6155 (pttm) REVERT: C 52 LYS cc_start: 0.7908 (mttt) cc_final: 0.7410 (mtmm) REVERT: C 90 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6302 (m) REVERT: C 198 ASN cc_start: 0.8038 (m-40) cc_final: 0.7649 (t0) REVERT: L 125 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: E 39 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7018 (tp) REVERT: F 23 CYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7595 (t) REVERT: F 67 TYR cc_start: 0.8064 (m-80) cc_final: 0.7328 (m-80) REVERT: G 38 TYR cc_start: 0.8566 (m-80) cc_final: 0.8246 (m-80) REVERT: G 125 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5953 (mm-30) outliers start: 42 outliers final: 29 residues processed: 208 average time/residue: 0.1074 time to fit residues: 34.8550 Evaluate side-chains 212 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 112 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.0370 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 441 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.162507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109622 restraints weight = 18001.875| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.67 r_work: 0.3090 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15957 Z= 0.208 Angle : 0.608 8.722 21699 Z= 0.307 Chirality : 0.045 0.162 2526 Planarity : 0.004 0.047 2757 Dihedral : 5.077 34.154 2652 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.25 % Allowed : 20.43 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.18), residues: 1974 helix: -0.47 (0.32), residues: 279 sheet: -0.58 (0.24), residues: 516 loop : -1.95 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 69 TYR 0.013 0.001 TYR E 38 PHE 0.017 0.002 PHE C 192 TRP 0.017 0.002 TRP C 158 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (15912) covalent geometry : angle 0.59917 / 0.30 (21591) SS BOND : bond 0.00577 / 0.39 ( 18) SS BOND : angle 2.17034 / 1.33 ( 36) hydrogen bonds : bond 0.02952 / 2.04 ( 425) hydrogen bonds : angle 4.55321 / 3.11 ( 1209) Misc. bond : bond 0.00057 / 0.03 ( 3) link_BETA1-4 : bond 0.00146 / 0.10 ( 6) link_BETA1-4 : angle 1.40745 / 0.90 ( 18) link_NAG-ASN : bond 0.00233 / 0.16 ( 18) link_NAG-ASN : angle 1.06856 / 0.71 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7025 (tttp) cc_final: 0.6156 (pttm) REVERT: A 52 LYS cc_start: 0.7945 (mttt) cc_final: 0.7466 (mtmm) REVERT: A 304 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7413 (tttp) REVERT: P 405 GLU cc_start: 0.8274 (pt0) cc_final: 0.7734 (pm20) REVERT: B 17 LYS cc_start: 0.6947 (tttp) cc_final: 0.6186 (pttm) REVERT: B 52 LYS cc_start: 0.7923 (mttt) cc_final: 0.7416 (mtmm) REVERT: B 129 LYS cc_start: 0.8608 (mttt) cc_final: 0.8174 (mtpp) REVERT: B 312 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7790 (mt-10) REVERT: Q 436 ASP cc_start: 0.7550 (m-30) cc_final: 0.7285 (t0) REVERT: C 17 LYS cc_start: 0.7030 (tttp) cc_final: 0.6225 (pttm) REVERT: C 52 LYS cc_start: 0.7981 (mttt) cc_final: 0.7536 (mtmm) REVERT: C 198 ASN cc_start: 0.8122 (m-40) cc_final: 0.7738 (t0) REVERT: L 125 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6455 (mm-30) REVERT: E 39 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7215 (tp) REVERT: F 23 CYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7661 (t) REVERT: F 67 TYR cc_start: 0.8131 (m-80) cc_final: 0.7319 (m-80) REVERT: G 38 TYR cc_start: 0.8673 (m-80) cc_final: 0.8352 (m-80) REVERT: G 125 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6277 (mm-30) outliers start: 38 outliers final: 33 residues processed: 209 average time/residue: 0.1043 time to fit residues: 34.4543 Evaluate side-chains 217 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain P residue 455 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 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 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110181 restraints weight = 17987.884| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.79 r_work: 0.3106 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15957 Z= 0.143 Angle : 0.558 8.604 21699 Z= 0.283 Chirality : 0.043 0.150 2526 Planarity : 0.004 0.047 2757 Dihedral : 4.902 34.515 2652 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.43 % Allowed : 20.25 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 1974 helix: -0.35 (0.32), residues: 279 sheet: -0.52 (0.24), residues: 516 loop : -1.89 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.014 0.001 TYR L 38 PHE 0.014 0.001 PHE C 192 TRP 0.016 0.002 TRP C 158 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (15912) covalent geometry : angle 0.55132 / 0.28 (21591) SS BOND : bond 0.00454 / 0.31 ( 18) SS BOND : angle 1.81058 / 1.11 ( 36) hydrogen bonds : bond 0.02643 / 1.83 ( 425) hydrogen bonds : angle 4.45596 / 3.04 ( 1209) Misc. bond : bond 0.00044 / 0.02 ( 3) link_BETA1-4 : bond 0.00195 / 0.14 ( 6) link_BETA1-4 : angle 1.25711 / 0.80 ( 18) link_NAG-ASN : bond 0.00172 / 0.12 ( 18) link_NAG-ASN : angle 0.90916 / 0.60 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.87 seconds wall clock time: 88 minutes 32.92 seconds (5312.92 seconds total)