Starting phenix.real_space_refine on Wed Mar 4 16:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.map" model { file = "/net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lue_23521/03_2026/7lue_23521.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 87 5.16 5 C 9474 2.51 5 N 2511 2.21 5 O 2946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15018 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "N" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 3.40, per 1000 atoms: 0.23 Number of scatterers: 15018 At special positions: 0 Unit cell: (131.15, 127.925, 123.625, 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 87 16.00 O 2946 8.00 N 2511 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 472.8 milliseconds 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 24.7% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.566A pdb=" N ILE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.565A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 492 through 506 Processing helix chain 'C' and resid 73 through 95 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.566A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 492 through 506 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.536A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.536A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 315 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 28 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU A 467 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.175A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 435 removed outlier: 6.688A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.156A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 315 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.156A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 28 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU B 467 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.176A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 435 removed outlier: 6.687A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 315 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE C 28 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU C 467 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.175A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 435 removed outlier: 6.688A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.475A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.476A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.475A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 1917 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: 2.60 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4824 1.34 - 1.46: 3361 1.46 - 1.58: 6971 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 15276 Sorted by residual: bond pdb=" CA THR N 29 " pdb=" C THR N 29 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.43e-02 4.89e+03 9.58e-01 bond pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta sigma weight residual 1.449 1.435 0.014 1.45e-02 4.76e+03 9.39e-01 bond pdb=" CG PRO A 246 " pdb=" CD PRO A 246 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.31e-01 bond pdb=" CA THR M 29 " pdb=" C THR M 29 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.43e-02 4.89e+03 9.25e-01 bond pdb=" CG PRO B 246 " pdb=" CD PRO B 246 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.03e-01 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 19280 0.87 - 1.74: 1219 1.74 - 2.60: 147 2.60 - 3.47: 66 3.47 - 4.34: 21 Bond angle restraints: 20733 Sorted by residual: angle pdb=" N GLY C 411 " pdb=" CA GLY C 411 " pdb=" C GLY C 411 " ideal model delta sigma weight residual 110.45 114.21 -3.76 1.30e+00 5.92e-01 8.38e+00 angle pdb=" N GLY A 411 " pdb=" CA GLY A 411 " pdb=" C GLY A 411 " ideal model delta sigma weight residual 110.45 114.18 -3.73 1.30e+00 5.92e-01 8.25e+00 angle pdb=" N GLY B 411 " pdb=" CA GLY B 411 " pdb=" C GLY B 411 " ideal model delta sigma weight residual 110.45 114.15 -3.70 1.30e+00 5.92e-01 8.11e+00 angle pdb=" N LYS M 50 " pdb=" CA LYS M 50 " pdb=" C LYS M 50 " ideal model delta sigma weight residual 109.41 105.54 3.87 1.52e+00 4.33e-01 6.47e+00 angle pdb=" N LYS N 50 " pdb=" CA LYS N 50 " pdb=" C LYS N 50 " ideal model delta sigma weight residual 109.41 105.56 3.85 1.52e+00 4.33e-01 6.42e+00 ... (remaining 20728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8902 17.84 - 35.69: 299 35.69 - 53.53: 63 53.53 - 71.37: 18 71.37 - 89.22: 12 Dihedral angle restraints: 9294 sinusoidal: 3627 harmonic: 5667 Sorted by residual: dihedral pdb=" CA LYS M 50 " pdb=" C LYS M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS N 50 " pdb=" C LYS N 50 " pdb=" N VAL N 51 " pdb=" CA VAL N 51 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS L 50 " pdb=" C LYS L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1567 0.031 - 0.062: 579 0.062 - 0.093: 168 0.093 - 0.124: 122 0.124 - 0.155: 15 Chirality restraints: 2451 Sorted by residual: chirality pdb=" CA ILE M 48 " pdb=" N ILE M 48 " pdb=" C ILE M 48 " pdb=" CB ILE M 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE N 48 " pdb=" N ILE N 48 " pdb=" C ILE N 48 " pdb=" CB ILE N 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2448 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 319 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 320 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 319 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 320 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 319 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 320 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.018 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1099 2.74 - 3.28: 14808 3.28 - 3.82: 25105 3.82 - 4.36: 32064 4.36 - 4.90: 55720 Nonbonded interactions: 128796 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.200 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.200 3.040 nonbonded pdb=" O ARG B 49 " pdb=" OG1 THR B 369 " model vdw 2.203 3.040 nonbonded pdb=" O ARG C 49 " pdb=" OG1 THR C 369 " model vdw 2.203 3.040 ... (remaining 128791 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 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.003 0.026 15303 Z= 0.144 Angle : 0.492 4.341 20787 Z= 0.295 Chirality : 0.041 0.155 2451 Planarity : 0.003 0.032 2610 Dihedral : 10.430 89.217 5559 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.86 % Allowed : 5.24 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1911 helix: 1.00 (0.27), residues: 369 sheet: 0.31 (0.20), residues: 639 loop : -0.04 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 235 TYR 0.012 0.001 TYR M 49 PHE 0.009 0.001 PHE J 100C TRP 0.007 0.001 TRP J 103 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00303 (15276) covalent geometry : angle 0.49162 (20733) SS BOND : bond 0.00184 ( 27) SS BOND : angle 0.65332 ( 54) hydrogen bonds : bond 0.21385 ( 720) hydrogen bonds : angle 8.82161 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 351 time to evaluate : 0.596 Fit side-chains REVERT: A 289 MET cc_start: 0.8420 (tpt) cc_final: 0.7901 (tpt) REVERT: A 448 ASP cc_start: 0.7611 (m-30) cc_final: 0.7136 (m-30) REVERT: B 448 ASP cc_start: 0.7693 (m-30) cc_final: 0.7469 (t0) REVERT: B 489 ASP cc_start: 0.6830 (t0) cc_final: 0.6428 (m-30) REVERT: B 493 SER cc_start: 0.7668 (t) cc_final: 0.7339 (p) REVERT: B 501 GLN cc_start: 0.7824 (mt0) cc_final: 0.7479 (mt0) REVERT: C 172 LEU cc_start: 0.8968 (tp) cc_final: 0.8649 (tp) REVERT: C 489 ASP cc_start: 0.7140 (t0) cc_final: 0.6631 (m-30) REVERT: C 493 SER cc_start: 0.7544 (t) cc_final: 0.7207 (p) REVERT: H 19 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7622 (tttt) REVERT: H 83 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8081 (p) REVERT: I 83 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8212 (p) REVERT: L 107 LYS cc_start: 0.5696 (mtmt) cc_final: 0.5475 (mtmm) REVERT: M 107 LYS cc_start: 0.6027 (mtmt) cc_final: 0.5823 (mtmm) REVERT: N 27 SER cc_start: 0.8087 (p) cc_final: 0.7857 (m) outliers start: 15 outliers final: 2 residues processed: 360 average time/residue: 0.6354 time to fit residues: 250.3390 Evaluate side-chains 245 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 241 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 202 GLN A 302 GLN A 345 ASN A 426 ASN B 27 ASN B 63 ASN B 183 ASN B 302 GLN B 331 ASN C 27 ASN C 63 ASN C 183 ASN C 197 ASN C 202 GLN C 208 ASN C 302 GLN C 426 ASN M 17 GLN N 30 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113302 restraints weight = 16660.424| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.54 r_work: 0.3231 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15303 Z= 0.128 Angle : 0.515 5.356 20787 Z= 0.281 Chirality : 0.044 0.154 2451 Planarity : 0.004 0.036 2610 Dihedral : 4.670 41.620 2076 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 11.23 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1911 helix: 1.83 (0.26), residues: 369 sheet: 0.55 (0.21), residues: 603 loop : -0.20 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 28 TYR 0.015 0.001 TYR M 49 PHE 0.011 0.001 PHE H 100C TRP 0.010 0.001 TRP A 314 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00284 (15276) covalent geometry : angle 0.51374 (20733) SS BOND : bond 0.00270 ( 27) SS BOND : angle 0.75914 ( 54) hydrogen bonds : bond 0.03761 ( 720) hydrogen bonds : angle 5.92571 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 0.682 Fit side-chains REVERT: A 77 LYS cc_start: 0.8027 (mmpt) cc_final: 0.7641 (mmtt) REVERT: A 289 MET cc_start: 0.8501 (tpt) cc_final: 0.8000 (tpt) REVERT: A 394 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7301 (ptpt) REVERT: B 77 LYS cc_start: 0.8121 (mttm) cc_final: 0.7397 (mmmt) REVERT: B 84 ASP cc_start: 0.7456 (m-30) cc_final: 0.7214 (m-30) REVERT: B 91 THR cc_start: 0.8633 (m) cc_final: 0.8365 (m) REVERT: B 163 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: B 208 ASN cc_start: 0.7471 (t0) cc_final: 0.7239 (t0) REVERT: B 235 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7826 (mtm-85) REVERT: B 448 ASP cc_start: 0.8053 (m-30) cc_final: 0.7677 (t0) REVERT: B 493 SER cc_start: 0.7821 (t) cc_final: 0.7254 (p) REVERT: B 501 GLN cc_start: 0.7959 (mt0) cc_final: 0.7595 (mt0) REVERT: C 77 LYS cc_start: 0.8151 (mttp) cc_final: 0.7516 (mmtt) REVERT: C 163 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: C 259 SER cc_start: 0.8681 (p) cc_final: 0.8424 (m) REVERT: C 378 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: C 493 SER cc_start: 0.7793 (t) cc_final: 0.7251 (p) REVERT: H 51 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8807 (tt) REVERT: I 38 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8372 (ttm-80) REVERT: I 46 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7756 (tt0) REVERT: I 72 ASP cc_start: 0.8596 (t0) cc_final: 0.8305 (t0) REVERT: I 82 SER cc_start: 0.8498 (m) cc_final: 0.7868 (t) REVERT: J 48 MET cc_start: 0.8615 (mtp) cc_final: 0.8412 (mtp) REVERT: L 107 LYS cc_start: 0.5398 (mtmt) cc_final: 0.5169 (mtmm) REVERT: M 7 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7888 (p) REVERT: M 107 LYS cc_start: 0.5900 (mtmt) cc_final: 0.5644 (mtmm) REVERT: N 7 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7926 (p) REVERT: N 24 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7863 (mtp-110) REVERT: N 54 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: N 100 GLN cc_start: 0.7778 (mp10) cc_final: 0.7330 (pm20) outliers start: 47 outliers final: 10 residues processed: 305 average time/residue: 0.5750 time to fit residues: 193.5069 Evaluate side-chains 240 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 139 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 162 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 426 ASN B 27 ASN B 63 ASN B 183 ASN B 345 ASN C 27 ASN C 63 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115236 restraints weight = 16762.529| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.54 r_work: 0.3175 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15303 Z= 0.126 Angle : 0.490 6.249 20787 Z= 0.265 Chirality : 0.043 0.159 2451 Planarity : 0.004 0.035 2610 Dihedral : 4.456 30.828 2073 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.57 % Allowed : 11.97 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1911 helix: 2.01 (0.26), residues: 372 sheet: 0.56 (0.21), residues: 603 loop : -0.26 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.017 0.001 TYR M 49 PHE 0.011 0.001 PHE H 100C TRP 0.010 0.001 TRP A 314 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00285 (15276) covalent geometry : angle 0.48945 (20733) SS BOND : bond 0.00194 ( 27) SS BOND : angle 0.77064 ( 54) hydrogen bonds : bond 0.03272 ( 720) hydrogen bonds : angle 5.46008 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.506 Fit side-chains REVERT: A 77 LYS cc_start: 0.8030 (mmpt) cc_final: 0.7633 (mmtt) REVERT: A 394 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7336 (ptpt) REVERT: A 448 ASP cc_start: 0.7919 (m-30) cc_final: 0.7555 (t0) REVERT: B 77 LYS cc_start: 0.8051 (mttm) cc_final: 0.7352 (mmmt) REVERT: B 84 ASP cc_start: 0.7400 (m-30) cc_final: 0.6944 (m-30) REVERT: B 163 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: B 208 ASN cc_start: 0.7483 (t0) cc_final: 0.7267 (t0) REVERT: B 235 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7916 (mtm-85) REVERT: B 336 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7031 (mtm-85) REVERT: B 493 SER cc_start: 0.7724 (t) cc_final: 0.7243 (p) REVERT: B 501 GLN cc_start: 0.8001 (mt0) cc_final: 0.7640 (mt0) REVERT: C 77 LYS cc_start: 0.8134 (mttp) cc_final: 0.7465 (mmtt) REVERT: C 163 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: C 448 ASP cc_start: 0.7901 (m-30) cc_final: 0.7644 (m-30) REVERT: C 493 SER cc_start: 0.7408 (t) cc_final: 0.6953 (p) REVERT: H 46 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7489 (tt0) REVERT: I 46 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7736 (tt0) REVERT: J 10 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: J 48 MET cc_start: 0.8684 (mtp) cc_final: 0.8437 (mtp) REVERT: L 107 LYS cc_start: 0.5481 (mtmt) cc_final: 0.5172 (mtmm) REVERT: M 50 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7662 (mttt) REVERT: M 107 LYS cc_start: 0.5966 (mtmt) cc_final: 0.5586 (mtmm) REVERT: N 7 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8027 (p) REVERT: N 24 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7848 (mtp-110) REVERT: N 54 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7842 (mtm-85) REVERT: N 70 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7242 (m) REVERT: N 100 GLN cc_start: 0.7799 (mp10) cc_final: 0.7404 (pm20) outliers start: 62 outliers final: 22 residues processed: 284 average time/residue: 0.6080 time to fit residues: 189.3003 Evaluate side-chains 252 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN B 331 ASN C 63 ASN C 345 ASN I 39 GLN J 39 GLN M 38 GLN N 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108602 restraints weight = 17017.881| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.54 r_work: 0.3080 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15303 Z= 0.277 Angle : 0.626 8.609 20787 Z= 0.334 Chirality : 0.047 0.174 2451 Planarity : 0.005 0.040 2610 Dihedral : 4.940 32.450 2071 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.89 % Allowed : 11.92 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1911 helix: 1.19 (0.25), residues: 396 sheet: 0.18 (0.20), residues: 582 loop : -0.67 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 282 TYR 0.028 0.002 TYR L 49 PHE 0.022 0.002 PHE H 100C TRP 0.016 0.002 TRP A 314 HIS 0.007 0.002 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00654 (15276) covalent geometry : angle 0.62394 (20733) SS BOND : bond 0.00357 ( 27) SS BOND : angle 1.13481 ( 54) hydrogen bonds : bond 0.03947 ( 720) hydrogen bonds : angle 5.75747 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 227 time to evaluate : 0.575 Fit side-chains REVERT: A 272 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7359 (ttmt) REVERT: A 426 ASN cc_start: 0.7730 (t0) cc_final: 0.7510 (t0) REVERT: B 163 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: B 235 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8182 (ttm-80) REVERT: B 493 SER cc_start: 0.7798 (t) cc_final: 0.7271 (p) REVERT: B 501 GLN cc_start: 0.7932 (mt0) cc_final: 0.7561 (mt0) REVERT: C 77 LYS cc_start: 0.8332 (mttp) cc_final: 0.7608 (mmtt) REVERT: C 163 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: C 272 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7232 (ttmt) REVERT: H 10 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: I 10 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: I 46 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7900 (tt0) REVERT: J 10 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: J 86 ASP cc_start: 0.7873 (m-30) cc_final: 0.7599 (m-30) REVERT: L 107 LYS cc_start: 0.5876 (mtmt) cc_final: 0.5539 (mtmm) REVERT: M 100 GLN cc_start: 0.7721 (mp10) cc_final: 0.7355 (pm20) REVERT: M 107 LYS cc_start: 0.6151 (mtmt) cc_final: 0.5549 (mtpm) REVERT: N 24 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7885 (mtp-110) REVERT: N 54 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: N 100 GLN cc_start: 0.7930 (mp10) cc_final: 0.7647 (pm20) outliers start: 85 outliers final: 44 residues processed: 284 average time/residue: 0.5741 time to fit residues: 180.0185 Evaluate side-chains 264 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN B 426 ASN C 63 ASN L 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112278 restraints weight = 16854.888| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.52 r_work: 0.3144 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15303 Z= 0.153 Angle : 0.524 7.753 20787 Z= 0.280 Chirality : 0.044 0.163 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.684 32.311 2071 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.91 % Allowed : 13.76 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1911 helix: 1.48 (0.25), residues: 396 sheet: 0.17 (0.20), residues: 582 loop : -0.62 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.018 0.002 TYR L 49 PHE 0.013 0.001 PHE H 100C TRP 0.011 0.001 TRP B 314 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00356 (15276) covalent geometry : angle 0.52316 (20733) SS BOND : bond 0.00205 ( 27) SS BOND : angle 0.73514 ( 54) hydrogen bonds : bond 0.03220 ( 720) hydrogen bonds : angle 5.43591 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 0.481 Fit side-chains REVERT: A 354 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: B 77 LYS cc_start: 0.8046 (mttm) cc_final: 0.7299 (mmmt) REVERT: B 163 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: B 235 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7999 (mtm-85) REVERT: B 289 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8459 (mmm) REVERT: B 354 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6772 (mp-120) REVERT: B 493 SER cc_start: 0.7652 (t) cc_final: 0.7186 (p) REVERT: B 501 GLN cc_start: 0.8004 (mt0) cc_final: 0.7645 (mt0) REVERT: C 77 LYS cc_start: 0.8251 (mttp) cc_final: 0.7557 (mmtt) REVERT: C 163 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 405 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8411 (t) REVERT: H 10 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: H 46 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7531 (tt0) REVERT: I 46 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7826 (tt0) REVERT: J 10 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: J 86 ASP cc_start: 0.7775 (m-30) cc_final: 0.7461 (m-30) REVERT: L 107 LYS cc_start: 0.5802 (mtmt) cc_final: 0.5372 (mtmm) REVERT: M 107 LYS cc_start: 0.6011 (mtmt) cc_final: 0.5576 (mtpm) REVERT: N 24 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7863 (mtp-110) REVERT: N 54 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7995 (ttp-110) REVERT: N 86 TYR cc_start: 0.8642 (m-80) cc_final: 0.8319 (m-80) REVERT: N 100 GLN cc_start: 0.7844 (mp10) cc_final: 0.7604 (pm20) outliers start: 68 outliers final: 32 residues processed: 278 average time/residue: 0.5636 time to fit residues: 173.5351 Evaluate side-chains 261 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 0.0980 chunk 134 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 197 ASN A 227 ASN A 426 ASN B 27 ASN B 63 ASN B 183 ASN C 371 ASN C 426 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111153 restraints weight = 16758.646| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.52 r_work: 0.3130 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15303 Z= 0.173 Angle : 0.537 7.939 20787 Z= 0.286 Chirality : 0.044 0.159 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.701 32.429 2071 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.15 % Allowed : 13.99 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1911 helix: 1.55 (0.25), residues: 396 sheet: 0.13 (0.20), residues: 582 loop : -0.64 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 61 TYR 0.020 0.002 TYR L 49 PHE 0.015 0.001 PHE H 100C TRP 0.012 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00405 (15276) covalent geometry : angle 0.53532 (20733) SS BOND : bond 0.00220 ( 27) SS BOND : angle 1.02194 ( 54) hydrogen bonds : bond 0.03264 ( 720) hydrogen bonds : angle 5.39432 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 0.590 Fit side-chains REVERT: A 394 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7025 (ptpt) REVERT: A 493 SER cc_start: 0.7139 (t) cc_final: 0.6653 (p) REVERT: B 77 LYS cc_start: 0.8071 (mttm) cc_final: 0.7318 (mmmt) REVERT: B 163 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: B 235 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8025 (mtm-85) REVERT: B 289 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8483 (mmm) REVERT: B 354 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.6814 (mp-120) REVERT: B 493 SER cc_start: 0.7799 (t) cc_final: 0.7370 (p) REVERT: B 501 GLN cc_start: 0.7989 (mt0) cc_final: 0.7625 (mt0) REVERT: C 63 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8116 (m-40) REVERT: C 77 LYS cc_start: 0.8233 (mttp) cc_final: 0.7547 (mmtt) REVERT: C 163 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 272 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7002 (ttmt) REVERT: C 405 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (t) REVERT: C 426 ASN cc_start: 0.7995 (t0) cc_final: 0.7733 (t0) REVERT: H 10 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: H 46 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7522 (tt0) REVERT: I 10 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: I 46 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7790 (tt0) REVERT: J 80 MET cc_start: 0.8501 (ttp) cc_final: 0.8298 (ttp) REVERT: J 86 ASP cc_start: 0.7841 (m-30) cc_final: 0.7464 (m-30) REVERT: M 24 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7153 (ttp80) REVERT: M 107 LYS cc_start: 0.6028 (mtmt) cc_final: 0.5581 (mtpm) REVERT: N 54 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.8046 (ttp-110) REVERT: N 86 TYR cc_start: 0.8674 (m-80) cc_final: 0.8385 (m-80) REVERT: N 100 GLN cc_start: 0.7823 (mp10) cc_final: 0.7612 (pm20) outliers start: 72 outliers final: 45 residues processed: 283 average time/residue: 0.5678 time to fit residues: 177.3508 Evaluate side-chains 274 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN I 54 ASN J 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113394 restraints weight = 16659.664| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.50 r_work: 0.3183 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15303 Z= 0.144 Angle : 0.515 7.951 20787 Z= 0.274 Chirality : 0.044 0.158 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.603 32.210 2071 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.68 % Allowed : 14.74 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1911 helix: 1.70 (0.25), residues: 396 sheet: 0.17 (0.20), residues: 582 loop : -0.61 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 24 TYR 0.017 0.001 TYR L 49 PHE 0.012 0.001 PHE H 100C TRP 0.010 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00334 (15276) covalent geometry : angle 0.51278 (20733) SS BOND : bond 0.00194 ( 27) SS BOND : angle 1.04672 ( 54) hydrogen bonds : bond 0.03062 ( 720) hydrogen bonds : angle 5.26876 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.636 Fit side-chains REVERT: A 394 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7324 (ptpt) REVERT: A 427 LYS cc_start: 0.7798 (tptm) cc_final: 0.6953 (pttm) REVERT: A 493 SER cc_start: 0.7204 (t) cc_final: 0.6735 (p) REVERT: B 77 LYS cc_start: 0.8015 (mttm) cc_final: 0.7280 (mmmt) REVERT: B 163 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: B 235 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7912 (mtm-85) REVERT: B 354 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.6806 (mp-120) REVERT: B 394 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7125 (ptpt) REVERT: B 493 SER cc_start: 0.7722 (t) cc_final: 0.7339 (p) REVERT: B 501 GLN cc_start: 0.7982 (mt0) cc_final: 0.7625 (mt0) REVERT: C 163 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: C 405 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8413 (t) REVERT: H 46 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7474 (tt0) REVERT: I 46 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7749 (tt0) REVERT: J 86 ASP cc_start: 0.7811 (m-30) cc_final: 0.7495 (m-30) REVERT: M 24 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7367 (mtp-110) REVERT: M 107 LYS cc_start: 0.6026 (mtmt) cc_final: 0.5578 (mtpm) REVERT: N 7 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8118 (p) REVERT: N 24 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7727 (mmm160) REVERT: N 54 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.8012 (ttp-110) outliers start: 64 outliers final: 40 residues processed: 280 average time/residue: 0.5756 time to fit residues: 178.4502 Evaluate side-chains 267 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 426 ASN C 500 ASN I 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112948 restraints weight = 16754.916| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.50 r_work: 0.3153 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15303 Z= 0.148 Angle : 0.517 8.498 20787 Z= 0.275 Chirality : 0.044 0.161 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.586 32.165 2071 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.97 % Allowed : 15.43 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1911 helix: 1.72 (0.25), residues: 396 sheet: 0.19 (0.20), residues: 582 loop : -0.61 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 24 TYR 0.018 0.002 TYR L 49 PHE 0.013 0.001 PHE H 100C TRP 0.011 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00345 (15276) covalent geometry : angle 0.51590 (20733) SS BOND : bond 0.00186 ( 27) SS BOND : angle 0.94704 ( 54) hydrogen bonds : bond 0.03062 ( 720) hydrogen bonds : angle 5.24223 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.535 Fit side-chains REVERT: A 394 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7322 (ptpt) REVERT: A 427 LYS cc_start: 0.7773 (tptm) cc_final: 0.7119 (pttp) REVERT: A 493 SER cc_start: 0.7194 (t) cc_final: 0.6739 (p) REVERT: B 77 LYS cc_start: 0.8045 (mttm) cc_final: 0.7317 (mmmt) REVERT: B 163 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: B 235 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8025 (ttm-80) REVERT: B 354 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6839 (mp-120) REVERT: B 394 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7133 (ptpt) REVERT: B 493 SER cc_start: 0.7643 (t) cc_final: 0.7292 (p) REVERT: B 501 GLN cc_start: 0.7969 (mt0) cc_final: 0.7613 (mt0) REVERT: C 63 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8008 (m110) REVERT: C 77 LYS cc_start: 0.8122 (mttp) cc_final: 0.7468 (mmtt) REVERT: C 163 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: C 272 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.6951 (ttmt) REVERT: C 405 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8420 (t) REVERT: C 426 ASN cc_start: 0.8022 (t0) cc_final: 0.7774 (t0) REVERT: H 10 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: H 46 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7489 (tt0) REVERT: H 100 MET cc_start: 0.8479 (mtt) cc_final: 0.8210 (mtt) REVERT: I 46 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7759 (tt0) REVERT: J 86 ASP cc_start: 0.7823 (m-30) cc_final: 0.7476 (m-30) REVERT: M 24 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7392 (mtp-110) REVERT: M 107 LYS cc_start: 0.6037 (mtmt) cc_final: 0.5585 (mtpm) REVERT: N 24 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7731 (mmm160) REVERT: N 54 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.8028 (ttp-110) outliers start: 69 outliers final: 50 residues processed: 282 average time/residue: 0.5782 time to fit residues: 180.4936 Evaluate side-chains 280 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 142 optimal weight: 0.0770 chunk 172 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 371 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 500 ASN I 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114530 restraints weight = 16704.406| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.60 r_work: 0.3172 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15303 Z= 0.118 Angle : 0.495 8.384 20787 Z= 0.263 Chirality : 0.043 0.161 2451 Planarity : 0.004 0.036 2610 Dihedral : 4.482 32.013 2071 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.74 % Allowed : 16.12 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1911 helix: 1.84 (0.26), residues: 396 sheet: 0.28 (0.20), residues: 582 loop : -0.57 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 24 TYR 0.015 0.001 TYR L 49 PHE 0.016 0.001 PHE C 505 TRP 0.011 0.001 TRP J 36 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00272 (15276) covalent geometry : angle 0.49371 (20733) SS BOND : bond 0.00159 ( 27) SS BOND : angle 0.80201 ( 54) hydrogen bonds : bond 0.02884 ( 720) hydrogen bonds : angle 5.12865 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.576 Fit side-chains REVERT: A 394 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7345 (ptpt) REVERT: A 427 LYS cc_start: 0.7656 (tptm) cc_final: 0.7032 (pttp) REVERT: A 493 SER cc_start: 0.7327 (t) cc_final: 0.6863 (p) REVERT: A 501 GLN cc_start: 0.8044 (mt0) cc_final: 0.7731 (mt0) REVERT: B 77 LYS cc_start: 0.8023 (mttm) cc_final: 0.7278 (mmmt) REVERT: B 163 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: B 235 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7963 (mtm-85) REVERT: B 354 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6823 (mp-120) REVERT: B 394 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7112 (ptpt) REVERT: B 493 SER cc_start: 0.7636 (t) cc_final: 0.7288 (p) REVERT: B 501 GLN cc_start: 0.7910 (mt0) cc_final: 0.7565 (mt0) REVERT: C 63 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7977 (m110) REVERT: C 77 LYS cc_start: 0.8064 (mttp) cc_final: 0.7403 (mmtt) REVERT: C 163 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: C 405 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8420 (t) REVERT: C 493 SER cc_start: 0.7317 (t) cc_final: 0.7023 (m) REVERT: H 46 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7481 (tt0) REVERT: H 83 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.7996 (p) REVERT: H 100 MET cc_start: 0.8413 (mtt) cc_final: 0.8193 (mtt) REVERT: I 46 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7753 (tt0) REVERT: J 86 ASP cc_start: 0.7756 (m-30) cc_final: 0.7395 (m-30) REVERT: M 24 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7381 (mtp-110) REVERT: M 107 LYS cc_start: 0.5959 (mtmt) cc_final: 0.5502 (mtpm) REVERT: N 54 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7985 (ttp-110) outliers start: 65 outliers final: 43 residues processed: 285 average time/residue: 0.5666 time to fit residues: 179.0842 Evaluate side-chains 272 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 88 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 500 ASN I 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110698 restraints weight = 16907.144| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.53 r_work: 0.3138 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15303 Z= 0.191 Angle : 0.557 8.950 20787 Z= 0.296 Chirality : 0.045 0.175 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.689 32.629 2071 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.22 % Allowed : 16.93 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1911 helix: 1.66 (0.25), residues: 396 sheet: 0.18 (0.20), residues: 582 loop : -0.66 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.023 0.002 TYR L 49 PHE 0.017 0.001 PHE H 100C TRP 0.013 0.002 TRP A 314 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00448 (15276) covalent geometry : angle 0.55429 (20733) SS BOND : bond 0.00253 ( 27) SS BOND : angle 1.24325 ( 54) hydrogen bonds : bond 0.03287 ( 720) hydrogen bonds : angle 5.32549 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.625 Fit side-chains REVERT: A 427 LYS cc_start: 0.7695 (tptm) cc_final: 0.7048 (pttp) REVERT: A 493 SER cc_start: 0.7200 (t) cc_final: 0.6743 (p) REVERT: A 501 GLN cc_start: 0.8040 (mt0) cc_final: 0.7732 (mt0) REVERT: B 77 LYS cc_start: 0.8041 (mttm) cc_final: 0.7271 (mmmt) REVERT: B 163 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: B 235 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8088 (mtm-85) REVERT: B 354 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6917 (mp-120) REVERT: B 493 SER cc_start: 0.7673 (t) cc_final: 0.7320 (p) REVERT: B 501 GLN cc_start: 0.7926 (mt0) cc_final: 0.7596 (mt0) REVERT: C 63 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7911 (m110) REVERT: C 77 LYS cc_start: 0.8128 (mttp) cc_final: 0.7466 (mmtt) REVERT: C 163 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: C 183 ASN cc_start: 0.7413 (m-40) cc_final: 0.7076 (m110) REVERT: C 272 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.6969 (ttmt) REVERT: C 405 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8404 (t) REVERT: C 498 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7716 (ttpt) REVERT: H 46 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7475 (tt0) REVERT: I 46 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7804 (tt0) REVERT: I 75 THR cc_start: 0.8670 (p) cc_final: 0.8381 (t) REVERT: J 83 THR cc_start: 0.8571 (m) cc_final: 0.8302 (m) REVERT: M 24 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7410 (mtp-110) REVERT: M 107 LYS cc_start: 0.5968 (mtmt) cc_final: 0.5505 (mtpm) REVERT: N 54 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8035 (ttp-110) outliers start: 56 outliers final: 43 residues processed: 269 average time/residue: 0.5417 time to fit residues: 161.3127 Evaluate side-chains 269 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 500 ASN I 54 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113334 restraints weight = 16689.239| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.51 r_work: 0.3150 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15303 Z= 0.139 Angle : 0.516 8.628 20787 Z= 0.274 Chirality : 0.044 0.158 2451 Planarity : 0.004 0.036 2610 Dihedral : 4.566 32.662 2071 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.22 % Allowed : 17.04 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1911 helix: 1.78 (0.26), residues: 396 sheet: 0.21 (0.20), residues: 582 loop : -0.62 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.016 0.001 TYR L 49 PHE 0.011 0.001 PHE H 100C TRP 0.011 0.001 TRP A 314 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00324 (15276) covalent geometry : angle 0.51437 (20733) SS BOND : bond 0.00186 ( 27) SS BOND : angle 0.99295 ( 54) hydrogen bonds : bond 0.03013 ( 720) hydrogen bonds : angle 5.20699 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5563.13 seconds wall clock time: 95 minutes 43.03 seconds (5743.03 seconds total)