Starting phenix.real_space_refine on Sat Aug 23 23:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvi_41643/08_2025/8tvi_41643.cif" } resolution = 3.2 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= 0.083 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 96 5.16 5 C 9832 2.51 5 N 2540 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3816 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 12, 'ASN:plan1': 5, 'ARG:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 2.65, per 1000 atoms: 0.17 Number of scatterers: 15324 At special positions: 0 Unit cell: (143.29, 143.29, 123.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 96 16.00 O 2852 8.00 N 2540 7.00 C 9832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 243 " distance=2.01 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 396 " distance=2.08 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.01 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.01 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.01 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.04 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.08 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.08 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 568 " - pdb=" SG CYS D 577 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 189 " " NAG B 701 " - " ASN B 189 " " NAG C 701 " - " ASN C 189 " " NAG D 701 " - " ASN D 189 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 639.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 548 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 194 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" ND1 HIS B 548 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 194 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" ND1 HIS C 548 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 194 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 548 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 194 " 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 19.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 141 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'C' and resid 69 through 86 Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 141 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL C 400 " --> pdb=" O CYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'D' and resid 69 through 86 Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.514A pdb=" N VAL D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.936A pdb=" N LYS D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.938A pdb=" N VAL D 400 " --> pdb=" O CYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 433 through 437 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 177 through 178 current: chain 'A' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 239 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A 222 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 237 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 250 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS A 240 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 248 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 251 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 275 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 253 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 273 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 255 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER A 299 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS A 285 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 297 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 287 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 295 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 339 current: chain 'A' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 360 through 370 current: chain 'A' and resid 405 through 418 Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 448 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER A 538 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 177 through 178 current: chain 'B' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 239 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN B 222 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 237 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 250 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE B 248 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 251 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER B 275 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 253 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 273 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 255 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER B 299 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 285 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 297 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 287 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP B 295 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 339 current: chain 'B' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 360 through 370 current: chain 'B' and resid 405 through 418 Processing sheet with id=AB2, first strand: chain 'B' and resid 443 through 448 Processing sheet with id=AB3, first strand: chain 'B' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER B 538 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 177 through 178 current: chain 'C' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR C 220 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG C 239 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN C 222 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU C 237 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 250 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 240 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 248 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 251 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER C 275 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 253 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 273 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 255 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER C 299 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS C 285 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 297 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 287 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP C 295 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 339 current: chain 'C' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 360 through 370 current: chain 'C' and resid 405 through 418 Processing sheet with id=AB8, first strand: chain 'C' and resid 443 through 448 Processing sheet with id=AB9, first strand: chain 'C' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER C 538 " --> pdb=" O ILE C 554 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 177 through 178 current: chain 'D' and resid 574 through 584 removed outlier: 4.582A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 227 removed outlier: 5.442A pdb=" N TYR D 220 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG D 239 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN D 222 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU D 237 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 250 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS D 240 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 248 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 251 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER D 275 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE D 253 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 273 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 255 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.848A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 339 current: chain 'D' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 360 through 370 current: chain 'D' and resid 405 through 418 Processing sheet with id=AC5, first strand: chain 'D' and resid 443 through 448 Processing sheet with id=AC6, first strand: chain 'D' and resid 514 through 516 removed outlier: 4.512A pdb=" N SER D 538 " --> pdb=" O ILE D 554 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1503 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: 2.19 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2740 1.32 - 1.45: 3940 1.45 - 1.57: 8832 1.57 - 1.70: 8 1.70 - 1.82: 136 Bond restraints: 15656 Sorted by residual: bond pdb=" C LYS D 103 " pdb=" O LYS D 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS B 103 " pdb=" O LYS B 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C LYS C 103 " pdb=" O LYS C 103 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C5 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 15651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 18440 1.63 - 3.26: 2368 3.26 - 4.90: 300 4.90 - 6.53: 148 6.53 - 8.16: 80 Bond angle restraints: 21336 Sorted by residual: angle pdb=" C PHE C 432 " pdb=" N PRO C 433 " pdb=" CA PRO C 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE D 432 " pdb=" N PRO D 433 " pdb=" CA PRO D 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C PHE A 432 " pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.20e-01 1.93e+00 7.93e+01 angle pdb=" C LYS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 119.24 127.40 -8.16 1.04e+00 9.25e-01 6.16e+01 ... (remaining 21331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 9120 17.51 - 35.02: 252 35.02 - 52.53: 48 52.53 - 70.05: 32 70.05 - 87.56: 8 Dihedral angle restraints: 9460 sinusoidal: 3484 harmonic: 5976 Sorted by residual: dihedral pdb=" CB CYS A 188 " pdb=" SG CYS A 188 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS C 188 " pdb=" SG CYS C 188 " pdb=" SG CYS C 604 " pdb=" CB CYS C 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.62 53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1712 0.058 - 0.116: 624 0.116 - 0.174: 136 0.174 - 0.232: 8 0.232 - 0.290: 4 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2 NAG D 701 " pdb=" C1 NAG D 701 " pdb=" C3 NAG D 701 " pdb=" N2 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2 NAG B 701 " pdb=" C1 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" N2 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2481 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 571 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR D 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 571 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 571 " 0.043 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR C 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 571 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 571 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 571 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 571 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 571 " 0.029 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 4 2.47 - 3.08: 10244 3.08 - 3.69: 21203 3.69 - 4.29: 33243 4.29 - 4.90: 55526 Nonbonded interactions: 120220 Sorted by model distance: nonbonded pdb=" OD2 ASP C 544 " pdb="ZN ZN C 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP D 544 " pdb="ZN ZN D 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP A 544 " pdb="ZN ZN A 702 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP B 544 " pdb="ZN ZN B 702 " model vdw 1.868 2.230 nonbonded pdb=" OG SER A 230 " pdb=" NH1 ARG A 257 " model vdw 2.546 3.120 ... (remaining 120215 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' selection = chain 'D' } 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: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.012 0.134 15696 Z= 0.683 Angle : 1.288 8.550 21404 Z= 0.895 Chirality : 0.060 0.290 2484 Planarity : 0.008 0.126 2712 Dihedral : 10.007 87.557 5544 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2028 helix: 1.39 (0.26), residues: 316 sheet: 0.68 (0.17), residues: 780 loop : -0.24 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 592 TYR 0.043 0.005 TYR A 571 PHE 0.020 0.005 PHE C 523 TRP 0.020 0.005 TRP B 318 HIS 0.003 0.001 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.01164 (15656) covalent geometry : angle 1.27172 (21336) SS BOND : bond 0.01945 ( 28) SS BOND : angle 4.06850 ( 56) hydrogen bonds : bond 0.18282 ( 553) hydrogen bonds : angle 7.07807 ( 1503) metal coordination : bond 0.11115 ( 8) link_NAG-ASN : bond 0.05506 ( 4) link_NAG-ASN : angle 2.59730 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.498 Fit side-chains REVERT: A 181 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 181 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 181 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 181 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7691 (mt-10) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1272 time to fit residues: 48.8737 Evaluate side-chains 140 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN B 601 GLN C 601 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092054 restraints weight = 17799.908| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.91 r_work: 0.2791 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15696 Z= 0.153 Angle : 0.539 4.364 21404 Z= 0.301 Chirality : 0.046 0.145 2484 Planarity : 0.004 0.040 2712 Dihedral : 4.756 21.068 2280 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.30 % Allowed : 3.63 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.18), residues: 2028 helix: 2.94 (0.27), residues: 316 sheet: 0.83 (0.18), residues: 772 loop : -0.31 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 398 TYR 0.015 0.002 TYR C 446 PHE 0.019 0.002 PHE B 523 TRP 0.012 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00371 (15656) covalent geometry : angle 0.53716 (21336) SS BOND : bond 0.00258 ( 28) SS BOND : angle 1.00761 ( 56) hydrogen bonds : bond 0.05375 ( 553) hydrogen bonds : angle 5.30851 ( 1503) metal coordination : bond 0.00868 ( 8) link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 1.07449 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.554 Fit side-chains REVERT: A 247 GLU cc_start: 0.8155 (tt0) cc_final: 0.7874 (tt0) REVERT: A 520 ASP cc_start: 0.8016 (t0) cc_final: 0.7724 (t0) REVERT: B 247 GLU cc_start: 0.8149 (tt0) cc_final: 0.7868 (tt0) REVERT: B 520 ASP cc_start: 0.8015 (t0) cc_final: 0.7731 (t0) REVERT: C 247 GLU cc_start: 0.8151 (tt0) cc_final: 0.7869 (tt0) REVERT: C 520 ASP cc_start: 0.8038 (t0) cc_final: 0.7749 (t0) REVERT: D 247 GLU cc_start: 0.8158 (tt0) cc_final: 0.7878 (tt0) REVERT: D 520 ASP cc_start: 0.8029 (t0) cc_final: 0.7739 (t0) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.1068 time to fit residues: 27.6067 Evaluate side-chains 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 147 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.090853 restraints weight = 17998.450| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.88 r_work: 0.2766 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15696 Z= 0.129 Angle : 0.486 4.540 21404 Z= 0.266 Chirality : 0.045 0.148 2484 Planarity : 0.004 0.039 2712 Dihedral : 4.396 17.222 2280 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.55 % Allowed : 3.89 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 2028 helix: 3.34 (0.26), residues: 320 sheet: 0.71 (0.19), residues: 772 loop : -0.49 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 463 TYR 0.015 0.001 TYR B 446 PHE 0.016 0.002 PHE B 523 TRP 0.012 0.001 TRP A 274 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00312 (15656) covalent geometry : angle 0.48433 (21336) SS BOND : bond 0.00247 ( 28) SS BOND : angle 0.85238 ( 56) hydrogen bonds : bond 0.04224 ( 553) hydrogen bonds : angle 4.94634 ( 1503) metal coordination : bond 0.00249 ( 8) link_NAG-ASN : bond 0.00207 ( 4) link_NAG-ASN : angle 0.83287 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.456 Fit side-chains REVERT: A 474 SER cc_start: 0.8782 (p) cc_final: 0.8305 (m) REVERT: A 520 ASP cc_start: 0.8172 (t0) cc_final: 0.7768 (t0) REVERT: B 474 SER cc_start: 0.8780 (p) cc_final: 0.8302 (m) REVERT: B 520 ASP cc_start: 0.8150 (t0) cc_final: 0.7741 (t0) REVERT: C 474 SER cc_start: 0.8780 (p) cc_final: 0.8303 (m) REVERT: C 520 ASP cc_start: 0.8168 (t0) cc_final: 0.7766 (t0) REVERT: D 474 SER cc_start: 0.8783 (p) cc_final: 0.8309 (m) REVERT: D 520 ASP cc_start: 0.8177 (t0) cc_final: 0.7774 (t0) outliers start: 24 outliers final: 16 residues processed: 172 average time/residue: 0.0958 time to fit residues: 25.7122 Evaluate side-chains 152 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 47 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 122 optimal weight: 0.0370 chunk 157 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN B 601 GLN C 601 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091692 restraints weight = 17870.128| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.90 r_work: 0.2772 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15696 Z= 0.112 Angle : 0.464 4.569 21404 Z= 0.251 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.037 2712 Dihedral : 4.188 17.155 2280 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.55 % Allowed : 5.44 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 2028 helix: 3.59 (0.26), residues: 320 sheet: 0.70 (0.19), residues: 756 loop : -0.62 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 463 TYR 0.014 0.001 TYR A 446 PHE 0.015 0.002 PHE B 523 TRP 0.011 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00267 (15656) covalent geometry : angle 0.46276 (21336) SS BOND : bond 0.00169 ( 28) SS BOND : angle 0.71541 ( 56) hydrogen bonds : bond 0.03710 ( 553) hydrogen bonds : angle 4.77368 ( 1503) metal coordination : bond 0.00213 ( 8) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 0.79282 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.430 Fit side-chains REVERT: A 410 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8410 (mt) REVERT: A 474 SER cc_start: 0.8842 (p) cc_final: 0.8393 (m) REVERT: A 520 ASP cc_start: 0.8244 (t0) cc_final: 0.7814 (t0) REVERT: A 603 MET cc_start: 0.8002 (mmt) cc_final: 0.7717 (mmt) REVERT: B 410 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 474 SER cc_start: 0.8842 (p) cc_final: 0.8394 (m) REVERT: B 520 ASP cc_start: 0.8246 (t0) cc_final: 0.7815 (t0) REVERT: B 603 MET cc_start: 0.8002 (mmt) cc_final: 0.7721 (mmt) REVERT: C 410 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 474 SER cc_start: 0.8842 (p) cc_final: 0.8397 (m) REVERT: C 520 ASP cc_start: 0.8245 (t0) cc_final: 0.7818 (t0) REVERT: C 603 MET cc_start: 0.8010 (mmt) cc_final: 0.7729 (mmt) REVERT: D 410 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8405 (mt) REVERT: D 474 SER cc_start: 0.8843 (p) cc_final: 0.8400 (m) REVERT: D 520 ASP cc_start: 0.8249 (t0) cc_final: 0.7818 (t0) REVERT: D 603 MET cc_start: 0.8011 (mmt) cc_final: 0.7728 (mmt) outliers start: 24 outliers final: 18 residues processed: 156 average time/residue: 0.1057 time to fit residues: 25.7067 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 199 optimal weight: 0.0970 chunk 180 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.089560 restraints weight = 18061.176| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.87 r_work: 0.2745 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15696 Z= 0.151 Angle : 0.495 4.547 21404 Z= 0.265 Chirality : 0.046 0.147 2484 Planarity : 0.004 0.037 2712 Dihedral : 4.268 16.800 2280 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.49 % Allowed : 5.76 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.19), residues: 2028 helix: 3.60 (0.26), residues: 320 sheet: 0.57 (0.19), residues: 748 loop : -0.76 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 463 TYR 0.016 0.001 TYR A 446 PHE 0.016 0.002 PHE B 523 TRP 0.011 0.001 TRP B 274 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00378 (15656) covalent geometry : angle 0.49386 (21336) SS BOND : bond 0.00230 ( 28) SS BOND : angle 0.81215 ( 56) hydrogen bonds : bond 0.04076 ( 553) hydrogen bonds : angle 4.77670 ( 1503) metal coordination : bond 0.00200 ( 8) link_NAG-ASN : bond 0.00135 ( 4) link_NAG-ASN : angle 0.82439 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.454 Fit side-chains REVERT: A 132 TYR cc_start: 0.6599 (m-10) cc_final: 0.6127 (m-10) REVERT: A 410 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 474 SER cc_start: 0.8902 (p) cc_final: 0.8496 (m) REVERT: A 520 ASP cc_start: 0.8268 (t0) cc_final: 0.7830 (t0) REVERT: B 132 TYR cc_start: 0.6602 (m-10) cc_final: 0.6132 (m-10) REVERT: B 410 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 474 SER cc_start: 0.8902 (p) cc_final: 0.8495 (m) REVERT: B 520 ASP cc_start: 0.8265 (t0) cc_final: 0.7826 (t0) REVERT: C 132 TYR cc_start: 0.6626 (m-10) cc_final: 0.6149 (m-10) REVERT: C 410 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8442 (mt) REVERT: C 474 SER cc_start: 0.8901 (p) cc_final: 0.8496 (m) REVERT: C 520 ASP cc_start: 0.8268 (t0) cc_final: 0.7830 (t0) REVERT: D 132 TYR cc_start: 0.6609 (m-10) cc_final: 0.6134 (m-10) REVERT: D 410 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 474 SER cc_start: 0.8902 (p) cc_final: 0.8500 (m) REVERT: D 520 ASP cc_start: 0.8266 (t0) cc_final: 0.7828 (t0) outliers start: 23 outliers final: 15 residues processed: 152 average time/residue: 0.0957 time to fit residues: 22.5960 Evaluate side-chains 147 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 127 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089886 restraints weight = 18046.466| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.88 r_work: 0.2748 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15696 Z= 0.125 Angle : 0.478 5.003 21404 Z= 0.255 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.185 16.462 2280 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.30 % Allowed : 6.74 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 2028 helix: 3.61 (0.26), residues: 320 sheet: 0.56 (0.19), residues: 748 loop : -0.78 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 599 TYR 0.014 0.001 TYR A 446 PHE 0.014 0.002 PHE B 523 TRP 0.010 0.001 TRP C 274 HIS 0.003 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00307 (15656) covalent geometry : angle 0.47712 (21336) SS BOND : bond 0.00177 ( 28) SS BOND : angle 0.69043 ( 56) hydrogen bonds : bond 0.03808 ( 553) hydrogen bonds : angle 4.71126 ( 1503) metal coordination : bond 0.00146 ( 8) link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 0.79704 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.629 Fit side-chains REVERT: A 132 TYR cc_start: 0.6602 (m-10) cc_final: 0.6100 (m-10) REVERT: A 410 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 474 SER cc_start: 0.8878 (p) cc_final: 0.8461 (m) REVERT: A 520 ASP cc_start: 0.8249 (t0) cc_final: 0.7818 (t0) REVERT: B 132 TYR cc_start: 0.6609 (m-10) cc_final: 0.6107 (m-10) REVERT: B 410 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 474 SER cc_start: 0.8878 (p) cc_final: 0.8460 (m) REVERT: B 520 ASP cc_start: 0.8248 (t0) cc_final: 0.7816 (t0) REVERT: C 132 TYR cc_start: 0.6629 (m-10) cc_final: 0.6121 (m-10) REVERT: C 410 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8398 (mt) REVERT: C 474 SER cc_start: 0.8878 (p) cc_final: 0.8463 (m) REVERT: C 520 ASP cc_start: 0.8251 (t0) cc_final: 0.7821 (t0) REVERT: D 132 TYR cc_start: 0.6615 (m-10) cc_final: 0.6107 (m-10) REVERT: D 410 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8398 (mt) REVERT: D 474 SER cc_start: 0.8878 (p) cc_final: 0.8465 (m) REVERT: D 520 ASP cc_start: 0.8257 (t0) cc_final: 0.7826 (t0) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.1008 time to fit residues: 24.3193 Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089854 restraints weight = 17974.479| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.87 r_work: 0.2749 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15696 Z= 0.126 Angle : 0.477 4.562 21404 Z= 0.255 Chirality : 0.045 0.145 2484 Planarity : 0.004 0.035 2712 Dihedral : 4.158 16.043 2280 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.55 % Allowed : 6.48 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 2028 helix: 3.65 (0.26), residues: 320 sheet: 0.51 (0.19), residues: 748 loop : -0.79 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 463 TYR 0.014 0.001 TYR B 446 PHE 0.014 0.002 PHE D 523 TRP 0.010 0.001 TRP B 274 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00309 (15656) covalent geometry : angle 0.47595 (21336) SS BOND : bond 0.00186 ( 28) SS BOND : angle 0.68163 ( 56) hydrogen bonds : bond 0.03771 ( 553) hydrogen bonds : angle 4.70345 ( 1503) metal coordination : bond 0.00174 ( 8) link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 0.79607 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.542 Fit side-chains REVERT: A 410 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 474 SER cc_start: 0.8894 (p) cc_final: 0.8488 (m) REVERT: A 520 ASP cc_start: 0.8263 (t0) cc_final: 0.7834 (t0) REVERT: B 410 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 474 SER cc_start: 0.8897 (p) cc_final: 0.8491 (m) REVERT: B 520 ASP cc_start: 0.8272 (t0) cc_final: 0.7839 (t0) REVERT: C 410 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 474 SER cc_start: 0.8895 (p) cc_final: 0.8493 (m) REVERT: C 520 ASP cc_start: 0.8266 (t0) cc_final: 0.7836 (t0) REVERT: D 410 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (mt) REVERT: D 474 SER cc_start: 0.8894 (p) cc_final: 0.8490 (m) REVERT: D 520 ASP cc_start: 0.8274 (t0) cc_final: 0.7846 (t0) outliers start: 24 outliers final: 16 residues processed: 160 average time/residue: 0.1067 time to fit residues: 26.4333 Evaluate side-chains 152 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 169 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 183 optimal weight: 0.0010 chunk 102 optimal weight: 8.9990 chunk 124 optimal weight: 0.2980 chunk 191 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN B 430 GLN C 430 GLN D 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.089672 restraints weight = 18066.889| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.87 r_work: 0.2747 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15696 Z= 0.125 Angle : 0.471 4.564 21404 Z= 0.253 Chirality : 0.045 0.145 2484 Planarity : 0.004 0.035 2712 Dihedral : 4.127 15.279 2280 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 7.06 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 2028 helix: 3.68 (0.26), residues: 320 sheet: 0.48 (0.19), residues: 748 loop : -0.79 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 463 TYR 0.014 0.001 TYR B 446 PHE 0.014 0.002 PHE C 523 TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00308 (15656) covalent geometry : angle 0.46984 (21336) SS BOND : bond 0.00170 ( 28) SS BOND : angle 0.68199 ( 56) hydrogen bonds : bond 0.03725 ( 553) hydrogen bonds : angle 4.67001 ( 1503) metal coordination : bond 0.00156 ( 8) link_NAG-ASN : bond 0.00123 ( 4) link_NAG-ASN : angle 0.79016 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.439 Fit side-chains REVERT: A 132 TYR cc_start: 0.6633 (m-10) cc_final: 0.6109 (m-10) REVERT: A 410 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 474 SER cc_start: 0.8895 (p) cc_final: 0.8498 (m) REVERT: A 520 ASP cc_start: 0.8267 (t0) cc_final: 0.7837 (t0) REVERT: A 603 MET cc_start: 0.8103 (mmt) cc_final: 0.7825 (mmt) REVERT: B 132 TYR cc_start: 0.6626 (m-10) cc_final: 0.6105 (m-10) REVERT: B 410 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 474 SER cc_start: 0.8897 (p) cc_final: 0.8501 (m) REVERT: B 520 ASP cc_start: 0.8280 (t0) cc_final: 0.7848 (t0) REVERT: B 603 MET cc_start: 0.8091 (mmt) cc_final: 0.7816 (mmt) REVERT: C 132 TYR cc_start: 0.6640 (m-10) cc_final: 0.6113 (m-10) REVERT: C 410 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 474 SER cc_start: 0.8897 (p) cc_final: 0.8505 (m) REVERT: C 520 ASP cc_start: 0.8276 (t0) cc_final: 0.7844 (t0) REVERT: C 603 MET cc_start: 0.8099 (mmt) cc_final: 0.7823 (mmt) REVERT: D 132 TYR cc_start: 0.6634 (m-10) cc_final: 0.6105 (m-10) REVERT: D 410 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (mt) REVERT: D 474 SER cc_start: 0.8897 (p) cc_final: 0.8504 (m) REVERT: D 520 ASP cc_start: 0.8280 (t0) cc_final: 0.7849 (t0) REVERT: D 603 MET cc_start: 0.8096 (mmt) cc_final: 0.7818 (mmt) outliers start: 23 outliers final: 19 residues processed: 156 average time/residue: 0.1024 time to fit residues: 24.4965 Evaluate side-chains 163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 81 optimal weight: 0.0980 chunk 166 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.090262 restraints weight = 17899.984| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.86 r_work: 0.2768 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15696 Z= 0.109 Angle : 0.462 4.588 21404 Z= 0.247 Chirality : 0.044 0.142 2484 Planarity : 0.003 0.036 2712 Dihedral : 4.056 15.155 2280 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.97 % Allowed : 7.38 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 2028 helix: 3.75 (0.26), residues: 320 sheet: 0.51 (0.20), residues: 748 loop : -0.79 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 463 TYR 0.013 0.001 TYR B 446 PHE 0.013 0.002 PHE A 523 TRP 0.010 0.001 TRP C 274 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00262 (15656) covalent geometry : angle 0.46092 (21336) SS BOND : bond 0.00171 ( 28) SS BOND : angle 0.60806 ( 56) hydrogen bonds : bond 0.03499 ( 553) hydrogen bonds : angle 4.61891 ( 1503) metal coordination : bond 0.00132 ( 8) link_NAG-ASN : bond 0.00124 ( 4) link_NAG-ASN : angle 0.76719 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.416 Fit side-chains REVERT: A 474 SER cc_start: 0.8889 (p) cc_final: 0.8491 (m) REVERT: A 520 ASP cc_start: 0.8245 (t0) cc_final: 0.7826 (t0) REVERT: A 603 MET cc_start: 0.8129 (mmt) cc_final: 0.7862 (mmt) REVERT: B 474 SER cc_start: 0.8889 (p) cc_final: 0.8493 (m) REVERT: B 520 ASP cc_start: 0.8255 (t0) cc_final: 0.7835 (t0) REVERT: B 603 MET cc_start: 0.8112 (mmt) cc_final: 0.7849 (mmt) REVERT: C 474 SER cc_start: 0.8889 (p) cc_final: 0.8497 (m) REVERT: C 520 ASP cc_start: 0.8255 (t0) cc_final: 0.7834 (t0) REVERT: C 603 MET cc_start: 0.8120 (mmt) cc_final: 0.7857 (mmt) REVERT: D 474 SER cc_start: 0.8887 (p) cc_final: 0.8495 (m) REVERT: D 520 ASP cc_start: 0.8259 (t0) cc_final: 0.7838 (t0) REVERT: D 603 MET cc_start: 0.8117 (mmt) cc_final: 0.7852 (mmt) outliers start: 15 outliers final: 15 residues processed: 152 average time/residue: 0.1125 time to fit residues: 26.4095 Evaluate side-chains 159 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 188 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.090230 restraints weight = 18000.037| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.89 r_work: 0.2753 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15696 Z= 0.120 Angle : 0.468 4.592 21404 Z= 0.250 Chirality : 0.045 0.144 2484 Planarity : 0.003 0.035 2712 Dihedral : 4.056 14.986 2280 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.23 % Allowed : 7.58 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2028 helix: 3.80 (0.26), residues: 320 sheet: 0.49 (0.20), residues: 748 loop : -0.81 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 463 TYR 0.014 0.001 TYR B 446 PHE 0.014 0.002 PHE C 523 TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00295 (15656) covalent geometry : angle 0.46709 (21336) SS BOND : bond 0.00152 ( 28) SS BOND : angle 0.64229 ( 56) hydrogen bonds : bond 0.03597 ( 553) hydrogen bonds : angle 4.60946 ( 1503) metal coordination : bond 0.00166 ( 8) link_NAG-ASN : bond 0.00119 ( 4) link_NAG-ASN : angle 0.77580 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.521 Fit side-chains REVERT: A 474 SER cc_start: 0.8896 (p) cc_final: 0.8506 (m) REVERT: A 520 ASP cc_start: 0.8270 (t0) cc_final: 0.7846 (t0) REVERT: A 603 MET cc_start: 0.8099 (mmt) cc_final: 0.7840 (mmt) REVERT: B 474 SER cc_start: 0.8895 (p) cc_final: 0.8506 (m) REVERT: B 520 ASP cc_start: 0.8279 (t0) cc_final: 0.7855 (t0) REVERT: B 603 MET cc_start: 0.8091 (mmt) cc_final: 0.7834 (mmt) REVERT: C 474 SER cc_start: 0.8897 (p) cc_final: 0.8514 (m) REVERT: C 520 ASP cc_start: 0.8283 (t0) cc_final: 0.7856 (t0) REVERT: C 603 MET cc_start: 0.8094 (mmt) cc_final: 0.7840 (mmt) REVERT: D 474 SER cc_start: 0.8896 (p) cc_final: 0.8511 (m) REVERT: D 520 ASP cc_start: 0.8287 (t0) cc_final: 0.7865 (t0) REVERT: D 603 MET cc_start: 0.8093 (mmt) cc_final: 0.7832 (mmt) outliers start: 19 outliers final: 19 residues processed: 156 average time/residue: 0.0982 time to fit residues: 23.7294 Evaluate side-chains 163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 245 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 57 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.089707 restraints weight = 17974.558| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.87 r_work: 0.2753 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15696 Z= 0.127 Angle : 0.475 4.658 21404 Z= 0.254 Chirality : 0.045 0.144 2484 Planarity : 0.003 0.035 2712 Dihedral : 4.075 15.011 2280 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.97 % Allowed : 7.84 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 2028 helix: 3.80 (0.26), residues: 320 sheet: 0.48 (0.20), residues: 748 loop : -0.83 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 463 TYR 0.014 0.001 TYR C 446 PHE 0.014 0.002 PHE A 523 TRP 0.010 0.001 TRP D 274 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00315 (15656) covalent geometry : angle 0.47422 (21336) SS BOND : bond 0.00183 ( 28) SS BOND : angle 0.66803 ( 56) hydrogen bonds : bond 0.03668 ( 553) hydrogen bonds : angle 4.61243 ( 1503) metal coordination : bond 0.00172 ( 8) link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 0.78571 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.57 seconds wall clock time: 60 minutes 40.30 seconds (3640.30 seconds total)