Starting phenix.real_space_refine on Fri Jun 13 19:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvi_41643/06_2025/8tvi_41643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvi_41643/06_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_41643/06_2025/8tvi_41643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvi_41643/06_2025/8tvi_41643.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvi_41643/06_2025/8tvi_41643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvi_41643/06_2025/8tvi_41643.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} 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: C, B, D Time building chain proxies: 9.15, per 1000 atoms: 0.60 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 C 188 " - pdb=" SG CYS C 604 " distance=2.04 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.01 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.01 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.01 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.08 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.08 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 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: 3.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.06 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: 5.50 Time building geometry restraints manager: 3.97 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 5.520 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.270 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.020 0.005 TRP B 318 HIS 0.003 0.001 HIS C 596 PHE 0.020 0.005 PHE C 523 TYR 0.043 0.005 TYR A 571 ARG 0.005 0.001 ARG C 592 Details of bonding type rmsd link_NAG-ASN : bond 0.05506 ( 4) link_NAG-ASN : angle 2.59730 ( 12) hydrogen bonds : bond 0.18282 ( 553) hydrogen bonds : angle 7.07807 ( 1503) metal coordination : bond 0.11115 ( 8) SS BOND : bond 0.01945 ( 28) SS BOND : angle 4.06850 ( 56) covalent geometry : bond 0.01164 (15656) covalent geometry : angle 1.27172 (21336) *********************** 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 : 2.057 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: 0.3313 time to fit residues: 127.2512 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 : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3287 r_free = 0.3287 target = 0.119906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.091833 restraints weight = 17726.512| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.90 r_work: 0.2788 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 0.043 15696 Z= 0.155 Angle : 0.548 4.465 21404 Z= 0.302 Chirality : 0.046 0.146 2484 Planarity : 0.004 0.039 2712 Dihedral : 4.789 21.380 2280 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2028 helix: 2.92 (0.27), residues: 316 sheet: 0.83 (0.18), residues: 772 loop : -0.32 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 274 HIS 0.004 0.001 HIS B 194 PHE 0.019 0.002 PHE B 523 TYR 0.016 0.002 TYR D 446 ARG 0.002 0.000 ARG D 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 1.05573 ( 12) hydrogen bonds : bond 0.05329 ( 553) hydrogen bonds : angle 5.29818 ( 1503) metal coordination : bond 0.00893 ( 8) SS BOND : bond 0.00261 ( 28) SS BOND : angle 0.94725 ( 56) covalent geometry : bond 0.00381 (15656) covalent geometry : angle 0.54591 (21336) *********************** 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 176 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 2.165 Fit side-chains REVERT: A 247 GLU cc_start: 0.8153 (tt0) cc_final: 0.7871 (tt0) REVERT: A 488 MET cc_start: 0.8745 (ttm) cc_final: 0.8482 (ttm) REVERT: A 520 ASP cc_start: 0.8101 (t0) cc_final: 0.7789 (t0) REVERT: B 247 GLU cc_start: 0.8147 (tt0) cc_final: 0.7866 (tt0) REVERT: B 488 MET cc_start: 0.8748 (ttm) cc_final: 0.8482 (ttm) REVERT: B 520 ASP cc_start: 0.8096 (t0) cc_final: 0.7789 (t0) REVERT: C 247 GLU cc_start: 0.8154 (tt0) cc_final: 0.7873 (tt0) REVERT: C 488 MET cc_start: 0.8740 (ttm) cc_final: 0.8474 (ttm) REVERT: C 520 ASP cc_start: 0.8119 (t0) cc_final: 0.7808 (t0) REVERT: D 247 GLU cc_start: 0.8160 (tt0) cc_final: 0.7880 (tt0) REVERT: D 488 MET cc_start: 0.8753 (ttm) cc_final: 0.8487 (ttm) REVERT: D 520 ASP cc_start: 0.8110 (t0) cc_final: 0.7797 (t0) outliers start: 20 outliers final: 16 residues processed: 168 average time/residue: 0.3737 time to fit residues: 95.4786 Evaluate side-chains 160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 157 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.120321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.092477 restraints weight = 17728.300| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.87 r_work: 0.2797 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15696 Z= 0.113 Angle : 0.469 4.526 21404 Z= 0.258 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.038 2712 Dihedral : 4.282 17.036 2280 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.30 % Allowed : 4.40 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2028 helix: 3.45 (0.26), residues: 320 sheet: 0.77 (0.19), residues: 772 loop : -0.44 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.003 0.001 HIS C 194 PHE 0.015 0.002 PHE B 523 TYR 0.013 0.001 TYR B 446 ARG 0.001 0.000 ARG A 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 0.78976 ( 12) hydrogen bonds : bond 0.03898 ( 553) hydrogen bonds : angle 4.89472 ( 1503) metal coordination : bond 0.00060 ( 8) SS BOND : bond 0.00232 ( 28) SS BOND : angle 0.80918 ( 56) covalent geometry : bond 0.00261 (15656) covalent geometry : angle 0.46775 (21336) *********************** 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: 20 poor density : 156 time to evaluate : 1.720 Fit side-chains REVERT: A 474 SER cc_start: 0.8793 (p) cc_final: 0.8294 (m) REVERT: A 520 ASP cc_start: 0.8145 (t0) cc_final: 0.7740 (t0) REVERT: B 474 SER cc_start: 0.8793 (p) cc_final: 0.8294 (m) REVERT: B 520 ASP cc_start: 0.8128 (t0) cc_final: 0.7727 (t0) REVERT: C 474 SER cc_start: 0.8795 (p) cc_final: 0.8295 (m) REVERT: C 520 ASP cc_start: 0.8152 (t0) cc_final: 0.7748 (t0) REVERT: D 474 SER cc_start: 0.8798 (p) cc_final: 0.8301 (m) REVERT: D 520 ASP cc_start: 0.8152 (t0) cc_final: 0.7747 (t0) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.3206 time to fit residues: 85.1815 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 : 2.629 ------------------------------------------------------------------------------- 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 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 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 410 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.119273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.091392 restraints weight = 17799.514| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.90 r_work: 0.2768 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2063 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= 0.133 Angle : 0.485 4.547 21404 Z= 0.261 Chirality : 0.045 0.145 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.274 17.291 2280 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 5.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 2028 helix: 3.51 (0.26), residues: 320 sheet: 0.72 (0.19), residues: 772 loop : -0.60 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 PHE 0.016 0.002 PHE A 523 TYR 0.016 0.001 TYR A 446 ARG 0.001 0.000 ARG C 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 4) link_NAG-ASN : angle 0.82642 ( 12) hydrogen bonds : bond 0.03955 ( 553) hydrogen bonds : angle 4.83653 ( 1503) metal coordination : bond 0.00142 ( 8) SS BOND : bond 0.00199 ( 28) SS BOND : angle 0.75313 ( 56) covalent geometry : bond 0.00328 (15656) covalent geometry : angle 0.48378 (21336) *********************** 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 160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.753 Fit side-chains REVERT: A 410 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8467 (mt) REVERT: A 474 SER cc_start: 0.8819 (p) cc_final: 0.8360 (m) REVERT: A 520 ASP cc_start: 0.8227 (t0) cc_final: 0.7802 (t0) REVERT: B 410 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8465 (mt) REVERT: B 474 SER cc_start: 0.8820 (p) cc_final: 0.8363 (m) REVERT: B 520 ASP cc_start: 0.8222 (t0) cc_final: 0.7798 (t0) REVERT: C 410 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 474 SER cc_start: 0.8818 (p) cc_final: 0.8363 (m) REVERT: C 520 ASP cc_start: 0.8225 (t0) cc_final: 0.7803 (t0) REVERT: D 410 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8464 (mt) REVERT: D 474 SER cc_start: 0.8820 (p) cc_final: 0.8367 (m) REVERT: D 520 ASP cc_start: 0.8240 (t0) cc_final: 0.7819 (t0) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.2516 time to fit residues: 61.0251 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 : 1.802 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 29 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 135 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.117289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.089492 restraints weight = 18182.302| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.88 r_work: 0.2744 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15696 Z= 0.142 Angle : 0.491 4.534 21404 Z= 0.265 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.285 16.968 2280 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.30 % Allowed : 5.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2028 helix: 3.57 (0.26), residues: 320 sheet: 0.54 (0.19), residues: 748 loop : -0.76 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.004 0.001 HIS B 194 PHE 0.015 0.002 PHE D 523 TYR 0.015 0.001 TYR B 446 ARG 0.002 0.000 ARG C 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 0.80427 ( 12) hydrogen bonds : bond 0.04070 ( 553) hydrogen bonds : angle 4.79921 ( 1503) metal coordination : bond 0.00190 ( 8) SS BOND : bond 0.00238 ( 28) SS BOND : angle 0.81816 ( 56) covalent geometry : bond 0.00353 (15656) covalent geometry : angle 0.48949 (21336) *********************** 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 160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.543 Fit side-chains REVERT: A 410 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 474 SER cc_start: 0.8894 (p) cc_final: 0.8480 (m) REVERT: A 488 MET cc_start: 0.8791 (ttm) cc_final: 0.8562 (ttm) REVERT: A 520 ASP cc_start: 0.8245 (t0) cc_final: 0.7813 (t0) REVERT: B 410 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8438 (mt) REVERT: B 474 SER cc_start: 0.8895 (p) cc_final: 0.8482 (m) REVERT: B 488 MET cc_start: 0.8802 (ttm) cc_final: 0.8573 (ttm) REVERT: B 520 ASP cc_start: 0.8238 (t0) cc_final: 0.7806 (t0) REVERT: C 410 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 474 SER cc_start: 0.8891 (p) cc_final: 0.8480 (m) REVERT: C 488 MET cc_start: 0.8789 (ttm) cc_final: 0.8560 (ttm) REVERT: C 520 ASP cc_start: 0.8245 (t0) cc_final: 0.7815 (t0) REVERT: D 410 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 474 SER cc_start: 0.8894 (p) cc_final: 0.8484 (m) REVERT: D 488 MET cc_start: 0.8791 (ttm) cc_final: 0.8562 (ttm) REVERT: D 520 ASP cc_start: 0.8253 (t0) cc_final: 0.7822 (t0) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.2497 time to fit residues: 60.4966 Evaluate side-chains 140 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 2.424 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 160 optimal weight: 0.0170 chunk 189 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 193 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.119631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091881 restraints weight = 18013.955| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.89 r_work: 0.2774 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: 0.8568 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15696 Z= 0.093 Angle : 0.445 4.601 21404 Z= 0.239 Chirality : 0.044 0.138 2484 Planarity : 0.003 0.033 2712 Dihedral : 4.012 16.051 2280 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.04 % Allowed : 6.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2028 helix: 3.74 (0.26), residues: 320 sheet: 0.60 (0.19), residues: 748 loop : -0.73 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.002 0.001 HIS B 194 PHE 0.012 0.002 PHE A 523 TYR 0.011 0.001 TYR C 446 ARG 0.001 0.000 ARG A 584 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 4) link_NAG-ASN : angle 0.74931 ( 12) hydrogen bonds : bond 0.03328 ( 553) hydrogen bonds : angle 4.62782 ( 1503) metal coordination : bond 0.00061 ( 8) SS BOND : bond 0.00135 ( 28) SS BOND : angle 0.56286 ( 56) covalent geometry : bond 0.00215 (15656) covalent geometry : angle 0.44425 (21336) *********************** 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: 16 poor density : 148 time to evaluate : 1.577 Fit side-chains REVERT: A 474 SER cc_start: 0.8845 (p) cc_final: 0.8394 (m) REVERT: A 520 ASP cc_start: 0.8251 (t0) cc_final: 0.7809 (t0) REVERT: A 603 MET cc_start: 0.8113 (mmt) cc_final: 0.7824 (mmt) REVERT: B 474 SER cc_start: 0.8846 (p) cc_final: 0.8392 (m) REVERT: B 520 ASP cc_start: 0.8255 (t0) cc_final: 0.7813 (t0) REVERT: B 603 MET cc_start: 0.8102 (mmt) cc_final: 0.7819 (mmt) REVERT: C 474 SER cc_start: 0.8846 (p) cc_final: 0.8399 (m) REVERT: C 520 ASP cc_start: 0.8263 (t0) cc_final: 0.7821 (t0) REVERT: C 603 MET cc_start: 0.8111 (mmt) cc_final: 0.7827 (mmt) REVERT: D 474 SER cc_start: 0.8844 (p) cc_final: 0.8394 (m) REVERT: D 520 ASP cc_start: 0.8270 (t0) cc_final: 0.7828 (t0) REVERT: D 603 MET cc_start: 0.8119 (mmt) cc_final: 0.7831 (mmt) outliers start: 16 outliers final: 16 residues processed: 156 average time/residue: 0.2552 time to fit residues: 61.5129 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 : 1.652 ------------------------------------------------------------------------------- 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 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 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 245 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.117423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.089756 restraints weight = 18028.735| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.87 r_work: 0.2770 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15696 Z= 0.137 Angle : 0.480 4.586 21404 Z= 0.257 Chirality : 0.045 0.146 2484 Planarity : 0.004 0.034 2712 Dihedral : 4.091 15.583 2280 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.42 % Allowed : 5.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 2028 helix: 3.70 (0.26), residues: 320 sheet: 0.53 (0.19), residues: 748 loop : -0.76 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS D 194 PHE 0.015 0.002 PHE A 523 TYR 0.015 0.001 TYR D 446 ARG 0.001 0.000 ARG C 584 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 4) link_NAG-ASN : angle 0.80051 ( 12) hydrogen bonds : bond 0.03765 ( 553) hydrogen bonds : angle 4.66365 ( 1503) metal coordination : bond 0.00200 ( 8) SS BOND : bond 0.00201 ( 28) SS BOND : angle 0.70991 ( 56) covalent geometry : bond 0.00340 (15656) covalent geometry : angle 0.47926 (21336) *********************** 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 170 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.610 Fit side-chains REVERT: A 410 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 474 SER cc_start: 0.8894 (p) cc_final: 0.8492 (m) REVERT: A 520 ASP cc_start: 0.8234 (t0) cc_final: 0.7807 (t0) REVERT: A 603 MET cc_start: 0.8126 (mmt) cc_final: 0.7842 (mmt) REVERT: B 410 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 474 SER cc_start: 0.8893 (p) cc_final: 0.8494 (m) REVERT: B 520 ASP cc_start: 0.8248 (t0) cc_final: 0.7819 (t0) REVERT: B 603 MET cc_start: 0.8121 (mmt) cc_final: 0.7844 (mmt) REVERT: C 410 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8399 (mt) REVERT: C 474 SER cc_start: 0.8890 (p) cc_final: 0.8492 (m) REVERT: C 520 ASP cc_start: 0.8244 (t0) cc_final: 0.7814 (t0) REVERT: C 603 MET cc_start: 0.8130 (mmt) cc_final: 0.7851 (mmt) REVERT: D 410 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8397 (mt) REVERT: D 474 SER cc_start: 0.8891 (p) cc_final: 0.8493 (m) REVERT: D 520 ASP cc_start: 0.8249 (t0) cc_final: 0.7820 (t0) REVERT: D 603 MET cc_start: 0.8127 (mmt) cc_final: 0.7846 (mmt) outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.2648 time to fit residues: 67.7010 Evaluate side-chains 166 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.865 ------------------------------------------------------------------------------- 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 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 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 112 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.117742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.090058 restraints weight = 17943.911| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.87 r_work: 0.2757 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2483 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= 0.121 Angle : 0.465 4.566 21404 Z= 0.250 Chirality : 0.045 0.143 2484 Planarity : 0.003 0.033 2712 Dihedral : 4.069 14.770 2280 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.17 % Allowed : 6.61 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 2028 helix: 3.72 (0.26), residues: 320 sheet: 0.53 (0.19), residues: 744 loop : -0.79 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.003 0.001 HIS B 194 PHE 0.014 0.002 PHE A 523 TYR 0.014 0.001 TYR C 446 ARG 0.001 0.000 ARG A 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 0.79142 ( 12) hydrogen bonds : bond 0.03668 ( 553) hydrogen bonds : angle 4.61927 ( 1503) metal coordination : bond 0.00151 ( 8) SS BOND : bond 0.00167 ( 28) SS BOND : angle 0.68002 ( 56) covalent geometry : bond 0.00296 (15656) covalent geometry : angle 0.46444 (21336) *********************** 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 162 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.584 Fit side-chains REVERT: A 410 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 474 SER cc_start: 0.8882 (p) cc_final: 0.8469 (m) REVERT: A 520 ASP cc_start: 0.8257 (t0) cc_final: 0.7821 (t0) REVERT: A 603 MET cc_start: 0.8128 (mmt) cc_final: 0.7841 (mmt) REVERT: B 410 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 474 SER cc_start: 0.8883 (p) cc_final: 0.8471 (m) REVERT: B 520 ASP cc_start: 0.8266 (t0) cc_final: 0.7827 (t0) REVERT: B 603 MET cc_start: 0.8119 (mmt) cc_final: 0.7836 (mmt) REVERT: C 410 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 474 SER cc_start: 0.8883 (p) cc_final: 0.8474 (m) REVERT: C 520 ASP cc_start: 0.8269 (t0) cc_final: 0.7830 (t0) REVERT: C 603 MET cc_start: 0.8130 (mmt) cc_final: 0.7846 (mmt) REVERT: D 410 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8357 (mt) REVERT: D 474 SER cc_start: 0.8883 (p) cc_final: 0.8473 (m) REVERT: D 520 ASP cc_start: 0.8271 (t0) cc_final: 0.7834 (t0) REVERT: D 603 MET cc_start: 0.8126 (mmt) cc_final: 0.7838 (mmt) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 0.2435 time to fit residues: 58.7921 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 245 THR 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 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 77 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 171 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.118764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.091140 restraints weight = 18006.907| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.88 r_work: 0.2776 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15696 Z= 0.095 Angle : 0.446 4.610 21404 Z= 0.239 Chirality : 0.044 0.139 2484 Planarity : 0.003 0.033 2712 Dihedral : 3.942 14.262 2280 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.30 % Allowed : 6.99 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2028 helix: 3.88 (0.26), residues: 320 sheet: 0.56 (0.19), residues: 744 loop : -0.76 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.002 0.001 HIS B 194 PHE 0.012 0.002 PHE A 523 TYR 0.012 0.001 TYR D 446 ARG 0.001 0.000 ARG C 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 0.73042 ( 12) hydrogen bonds : bond 0.03304 ( 553) hydrogen bonds : angle 4.54175 ( 1503) metal coordination : bond 0.00097 ( 8) SS BOND : bond 0.00150 ( 28) SS BOND : angle 0.54135 ( 56) covalent geometry : bond 0.00223 (15656) covalent geometry : angle 0.44574 (21336) *********************** 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 172 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.833 Fit side-chains REVERT: A 410 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8317 (mt) REVERT: A 474 SER cc_start: 0.8874 (p) cc_final: 0.8456 (m) REVERT: A 520 ASP cc_start: 0.8263 (t0) cc_final: 0.7827 (t0) REVERT: B 410 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 474 SER cc_start: 0.8873 (p) cc_final: 0.8457 (m) REVERT: B 520 ASP cc_start: 0.8272 (t0) cc_final: 0.7837 (t0) REVERT: C 410 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8331 (mt) REVERT: C 474 SER cc_start: 0.8875 (p) cc_final: 0.8463 (m) REVERT: C 520 ASP cc_start: 0.8274 (t0) cc_final: 0.7836 (t0) REVERT: D 410 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8323 (mt) REVERT: D 474 SER cc_start: 0.8874 (p) cc_final: 0.8459 (m) REVERT: D 520 ASP cc_start: 0.8277 (t0) cc_final: 0.7841 (t0) outliers start: 20 outliers final: 12 residues processed: 168 average time/residue: 0.2659 time to fit residues: 69.2962 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 : 1.847 ------------------------------------------------------------------------------- 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 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 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 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 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3237 r_free = 0.3237 target = 0.115798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.088014 restraints weight = 18251.320| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.88 r_work: 0.2728 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15696 Z= 0.188 Angle : 0.526 4.575 21404 Z= 0.281 Chirality : 0.046 0.152 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.252 14.645 2280 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.10 % Allowed : 6.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2028 helix: 3.67 (0.26), residues: 320 sheet: 0.38 (0.20), residues: 748 loop : -0.91 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.004 0.001 HIS A 194 PHE 0.017 0.003 PHE A 523 TYR 0.019 0.002 TYR B 446 ARG 0.001 0.000 ARG B 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 0.90877 ( 12) hydrogen bonds : bond 0.04316 ( 553) hydrogen bonds : angle 4.73268 ( 1503) metal coordination : bond 0.00310 ( 8) SS BOND : bond 0.00236 ( 28) SS BOND : angle 0.92028 ( 56) covalent geometry : bond 0.00475 (15656) covalent geometry : angle 0.52456 (21336) ********************** 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 153 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.775 Fit side-chains REVERT: A 410 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 474 SER cc_start: 0.8894 (p) cc_final: 0.8506 (m) REVERT: A 501 MET cc_start: 0.8926 (mmt) cc_final: 0.8023 (mmt) REVERT: A 520 ASP cc_start: 0.8285 (t0) cc_final: 0.7834 (t0) REVERT: A 603 MET cc_start: 0.8070 (mmt) cc_final: 0.7785 (mmt) REVERT: B 410 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 474 SER cc_start: 0.8894 (p) cc_final: 0.8507 (m) REVERT: B 501 MET cc_start: 0.8933 (mmt) cc_final: 0.8024 (mmt) REVERT: B 520 ASP cc_start: 0.8291 (t0) cc_final: 0.7841 (t0) REVERT: B 603 MET cc_start: 0.8066 (mmt) cc_final: 0.7785 (mmt) REVERT: C 410 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (mt) REVERT: C 474 SER cc_start: 0.8896 (p) cc_final: 0.8510 (m) REVERT: C 501 MET cc_start: 0.8927 (mmt) cc_final: 0.8023 (mmt) REVERT: C 520 ASP cc_start: 0.8301 (t0) cc_final: 0.7850 (t0) REVERT: C 603 MET cc_start: 0.8073 (mmt) cc_final: 0.7792 (mmt) REVERT: D 410 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8388 (mt) REVERT: D 474 SER cc_start: 0.8896 (p) cc_final: 0.8511 (m) REVERT: D 501 MET cc_start: 0.8931 (mmt) cc_final: 0.8022 (mmt) REVERT: D 520 ASP cc_start: 0.8308 (t0) cc_final: 0.7859 (t0) REVERT: D 603 MET cc_start: 0.8068 (mmt) cc_final: 0.7781 (mmt) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.2885 time to fit residues: 68.4684 Evaluate side-chains 149 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN 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 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 128 GLN 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 201 VAL Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.116651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.088935 restraints weight = 18030.574| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.86 r_work: 0.2743 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2580 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= 0.142 Angle : 0.490 4.567 21404 Z= 0.263 Chirality : 0.045 0.145 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.193 14.664 2280 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.84 % Allowed : 7.45 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2028 helix: 3.68 (0.26), residues: 320 sheet: 0.39 (0.20), residues: 748 loop : -0.92 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 PHE 0.015 0.002 PHE A 523 TYR 0.015 0.001 TYR B 446 ARG 0.001 0.000 ARG C 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 0.81354 ( 12) hydrogen bonds : bond 0.03974 ( 553) hydrogen bonds : angle 4.69641 ( 1503) metal coordination : bond 0.00214 ( 8) SS BOND : bond 0.00212 ( 28) SS BOND : angle 0.72947 ( 56) covalent geometry : bond 0.00351 (15656) covalent geometry : angle 0.48947 (21336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8679.51 seconds wall clock time: 154 minutes 53.34 seconds (9293.34 seconds total)