Starting phenix.real_space_refine on Mon Nov 18 03:38:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_41643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_41643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_41643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_41643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvi_41643/11_2024/8tvi_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.41, per 1000 atoms: 0.61 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=7, 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 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: 3.80 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: 1.82 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: 5.13 Time building geometry restraints manager: 4.46 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: 9099 17.51 - 35.02: 222 35.02 - 52.53: 39 52.53 - 70.05: 29 70.05 - 87.56: 8 Dihedral angle restraints: 9397 sinusoidal: 3421 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 A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 396 " pdb=" CB CYS A 396 " ideal model delta sinusoidal sigma weight residual 93.00 51.86 41.14 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 502 " pdb=" CB CYS A 502 " ideal model delta sinusoidal sigma weight residual 93.00 125.24 -32.24 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 9394 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: 25 2.47 - 3.08: 10265 3.08 - 3.69: 21224 3.69 - 4.29: 33243 4.29 - 4.90: 55526 Nonbonded interactions: 120283 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=" SG CYS B 219 " pdb=" SG CYS B 243 " model vdw 2.013 3.760 ... (remaining 120278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.830 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.870 ------------------------------------------------------------------------------- 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 0.065 15656 Z= 0.761 Angle : 1.272 8.162 21336 Z= 0.891 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 *********************** 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 : 1.768 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: 0.3299 time to fit residues: 126.4051 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 : 1.877 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15656 Z= 0.254 Angle : 0.544 4.355 21336 Z= 0.301 Chirality : 0.046 0.150 2484 Planarity : 0.004 0.040 2712 Dihedral : 4.867 23.048 2280 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.96 (0.18), residues: 2028 helix: 2.95 (0.26), residues: 316 sheet: 0.83 (0.18), residues: 772 loop : -0.30 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 274 HIS 0.004 0.001 HIS B 194 PHE 0.020 0.003 PHE A 523 TYR 0.016 0.002 TYR A 446 ARG 0.002 0.000 ARG C 398 *********************** 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 179 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.823 Fit side-chains REVERT: A 520 ASP cc_start: 0.7025 (t0) cc_final: 0.6803 (t0) REVERT: B 501 MET cc_start: 0.8606 (tpp) cc_final: 0.8168 (mmt) REVERT: B 520 ASP cc_start: 0.7006 (t0) cc_final: 0.6795 (t0) REVERT: C 501 MET cc_start: 0.8607 (tpp) cc_final: 0.8170 (mmt) REVERT: C 520 ASP cc_start: 0.7010 (t0) cc_final: 0.6801 (t0) REVERT: D 501 MET cc_start: 0.8608 (tpp) cc_final: 0.8168 (mmt) REVERT: D 520 ASP cc_start: 0.7021 (t0) cc_final: 0.6801 (t0) outliers start: 20 outliers final: 16 residues processed: 171 average time/residue: 0.2997 time to fit residues: 76.5573 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 200 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15656 Z= 0.199 Angle : 0.484 4.422 21336 Z= 0.266 Chirality : 0.045 0.144 2484 Planarity : 0.004 0.038 2712 Dihedral : 4.442 19.385 2280 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.30 % Allowed : 4.15 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.50 (0.26), residues: 316 sheet: 0.78 (0.19), residues: 772 loop : -0.44 (0.20), residues: 940 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 A 523 TYR 0.015 0.001 TYR A 446 ARG 0.002 0.000 ARG D 398 *********************** 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 181 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.738 Fit side-chains REVERT: A 520 ASP cc_start: 0.7122 (t0) cc_final: 0.6871 (t0) REVERT: B 398 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: B 501 MET cc_start: 0.8553 (tpp) cc_final: 0.8332 (mmt) REVERT: B 520 ASP cc_start: 0.7096 (t0) cc_final: 0.6866 (t0) REVERT: C 398 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: C 501 MET cc_start: 0.8550 (tpp) cc_final: 0.8329 (mmt) REVERT: C 520 ASP cc_start: 0.7099 (t0) cc_final: 0.6873 (t0) REVERT: D 398 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8043 (mtm-85) REVERT: D 501 MET cc_start: 0.8549 (tpp) cc_final: 0.8329 (mmt) REVERT: D 520 ASP cc_start: 0.7116 (t0) cc_final: 0.6872 (t0) outliers start: 20 outliers final: 12 residues processed: 177 average time/residue: 0.2827 time to fit residues: 75.0882 Evaluate side-chains 147 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU 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 410 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15656 Z= 0.177 Angle : 0.467 4.595 21336 Z= 0.253 Chirality : 0.044 0.147 2484 Planarity : 0.004 0.037 2712 Dihedral : 4.294 18.567 2280 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.36 % Allowed : 6.54 % Favored : 92.10 % 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: 0.91 (0.19), residues: 2028 helix: 3.54 (0.26), residues: 320 sheet: 0.78 (0.19), residues: 756 loop : -0.58 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS B 194 PHE 0.015 0.002 PHE A 523 TYR 0.014 0.001 TYR A 446 ARG 0.001 0.000 ARG D 463 *********************** 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 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.696 Fit side-chains REVERT: A 410 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 520 ASP cc_start: 0.7195 (t0) cc_final: 0.6948 (t0) REVERT: B 398 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: B 410 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8489 (mt) REVERT: B 520 ASP cc_start: 0.7168 (t0) cc_final: 0.6939 (t0) REVERT: C 398 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8042 (mtm-85) REVERT: C 410 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8483 (mt) REVERT: C 520 ASP cc_start: 0.7173 (t0) cc_final: 0.6951 (t0) REVERT: D 398 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: D 410 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8489 (mt) REVERT: D 520 ASP cc_start: 0.7187 (t0) cc_final: 0.6946 (t0) outliers start: 21 outliers final: 17 residues processed: 157 average time/residue: 0.2937 time to fit residues: 70.1938 Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL 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 201 VAL 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 201 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.0570 chunk 111 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 168 optimal weight: 0.0370 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15656 Z= 0.142 Angle : 0.452 4.613 21336 Z= 0.242 Chirality : 0.044 0.145 2484 Planarity : 0.003 0.035 2712 Dihedral : 4.102 17.772 2280 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.55 % Allowed : 6.48 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.19), residues: 2028 helix: 3.67 (0.26), residues: 320 sheet: 0.80 (0.19), residues: 756 loop : -0.61 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.003 0.001 HIS C 312 PHE 0.012 0.002 PHE C 523 TYR 0.012 0.001 TYR C 464 ARG 0.001 0.000 ARG B 463 *********************** 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 173 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.627 Fit side-chains REVERT: A 410 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 520 ASP cc_start: 0.7096 (t0) cc_final: 0.6873 (t0) REVERT: B 410 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8436 (mt) REVERT: B 520 ASP cc_start: 0.7075 (t0) cc_final: 0.6865 (t0) REVERT: C 410 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 520 ASP cc_start: 0.7077 (t0) cc_final: 0.6870 (t0) REVERT: D 410 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (mt) REVERT: D 520 ASP cc_start: 0.7090 (t0) cc_final: 0.6866 (t0) outliers start: 24 outliers final: 20 residues processed: 165 average time/residue: 0.2732 time to fit residues: 67.7914 Evaluate side-chains 162 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 A residue 447 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 447 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN C 430 GLN D 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15656 Z= 0.357 Angle : 0.549 4.558 21336 Z= 0.293 Chirality : 0.047 0.152 2484 Planarity : 0.004 0.038 2712 Dihedral : 4.506 17.946 2280 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.55 % Allowed : 7.25 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.19), residues: 2028 helix: 3.50 (0.27), residues: 320 sheet: 0.57 (0.19), residues: 748 loop : -0.78 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 274 HIS 0.005 0.002 HIS A 194 PHE 0.018 0.003 PHE D 317 TYR 0.020 0.002 TYR C 446 ARG 0.002 0.000 ARG A 463 *********************** 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 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.729 Fit side-chains REVERT: A 410 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 501 MET cc_start: 0.8627 (mmt) cc_final: 0.8122 (mmt) REVERT: A 520 ASP cc_start: 0.7187 (t0) cc_final: 0.6947 (t0) REVERT: B 410 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8533 (mt) REVERT: B 520 ASP cc_start: 0.7162 (t0) cc_final: 0.6934 (t0) REVERT: C 410 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 520 ASP cc_start: 0.7164 (t0) cc_final: 0.6941 (t0) REVERT: D 410 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8529 (mt) REVERT: D 520 ASP cc_start: 0.7181 (t0) cc_final: 0.6940 (t0) outliers start: 24 outliers final: 12 residues processed: 154 average time/residue: 0.2879 time to fit residues: 67.2311 Evaluate side-chains 144 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 A residue 477 SER 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 B residue 477 SER 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 C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15656 Z= 0.197 Angle : 0.477 4.552 21336 Z= 0.256 Chirality : 0.045 0.145 2484 Planarity : 0.003 0.035 2712 Dihedral : 4.291 17.532 2280 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.23 % Allowed : 7.90 % Favored : 90.87 % 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: 3.60 (0.27), residues: 320 sheet: 0.56 (0.20), residues: 748 loop : -0.76 (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 A 194 PHE 0.014 0.002 PHE A 523 TYR 0.013 0.001 TYR A 446 ARG 0.001 0.000 ARG A 398 *********************** 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 155 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.791 Fit side-chains REVERT: A 410 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 520 ASP cc_start: 0.7160 (t0) cc_final: 0.6939 (t0) REVERT: B 410 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 520 ASP cc_start: 0.7140 (t0) cc_final: 0.6927 (t0) REVERT: C 410 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (mt) REVERT: C 520 ASP cc_start: 0.7147 (t0) cc_final: 0.6940 (t0) REVERT: D 410 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8464 (mt) REVERT: D 520 ASP cc_start: 0.7161 (t0) cc_final: 0.6939 (t0) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2587 time to fit residues: 61.1806 Evaluate side-chains 151 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 477 SER 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 B residue 477 SER 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 C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15656 Z= 0.234 Angle : 0.488 4.565 21336 Z= 0.262 Chirality : 0.045 0.147 2484 Planarity : 0.004 0.036 2712 Dihedral : 4.281 17.138 2280 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.36 % Allowed : 7.77 % Favored : 90.87 % 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: 0.63 (0.19), residues: 2028 helix: 3.61 (0.27), residues: 320 sheet: 0.51 (0.20), residues: 748 loop : -0.78 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.003 0.001 HIS A 194 PHE 0.014 0.002 PHE A 523 TYR 0.015 0.001 TYR A 446 ARG 0.001 0.000 ARG B 463 *********************** 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 153 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 2.096 Fit side-chains REVERT: A 410 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 501 MET cc_start: 0.8635 (mmt) cc_final: 0.8140 (mmt) REVERT: A 520 ASP cc_start: 0.7176 (t0) cc_final: 0.6945 (t0) REVERT: B 410 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8482 (mt) REVERT: B 520 ASP cc_start: 0.7151 (t0) cc_final: 0.6941 (t0) REVERT: C 410 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8477 (mt) REVERT: C 520 ASP cc_start: 0.7158 (t0) cc_final: 0.6948 (t0) REVERT: D 410 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8482 (mt) REVERT: D 520 ASP cc_start: 0.7174 (t0) cc_final: 0.6949 (t0) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.2819 time to fit residues: 67.2888 Evaluate side-chains 149 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 477 SER 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 B residue 477 SER 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 C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.6980 chunk 171 optimal weight: 0.0010 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15656 Z= 0.195 Angle : 0.472 4.581 21336 Z= 0.253 Chirality : 0.045 0.145 2484 Planarity : 0.003 0.036 2712 Dihedral : 4.180 16.836 2280 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.91 % Allowed : 8.29 % Favored : 90.80 % 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: 3.68 (0.27), residues: 320 sheet: 0.54 (0.20), residues: 748 loop : -0.78 (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 A 194 PHE 0.014 0.002 PHE A 523 TYR 0.014 0.001 TYR A 446 ARG 0.001 0.000 ARG C 463 *********************** 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 155 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.702 Fit side-chains REVERT: A 520 ASP cc_start: 0.7175 (t0) cc_final: 0.6959 (t0) REVERT: B 520 ASP cc_start: 0.7166 (t0) cc_final: 0.6961 (t0) REVERT: C 520 ASP cc_start: 0.7170 (t0) cc_final: 0.6967 (t0) REVERT: D 520 ASP cc_start: 0.7187 (t0) cc_final: 0.6965 (t0) outliers start: 14 outliers final: 13 residues processed: 154 average time/residue: 0.2717 time to fit residues: 64.6458 Evaluate side-chains 150 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 477 SER 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 477 SER Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 134 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15656 Z= 0.148 Angle : 0.451 4.632 21336 Z= 0.240 Chirality : 0.044 0.141 2484 Planarity : 0.003 0.036 2712 Dihedral : 3.996 15.784 2280 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.84 % Allowed : 8.68 % Favored : 90.48 % 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: 0.76 (0.19), residues: 2028 helix: 3.82 (0.26), residues: 320 sheet: 0.58 (0.20), residues: 748 loop : -0.72 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 274 HIS 0.002 0.000 HIS A 194 PHE 0.012 0.002 PHE A 523 TYR 0.012 0.001 TYR A 446 ARG 0.001 0.000 ARG D 463 ********************** 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 167 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.697 Fit side-chains REVERT: A 520 ASP cc_start: 0.7188 (t0) cc_final: 0.6987 (t0) REVERT: D 520 ASP cc_start: 0.7190 (t0) cc_final: 0.6974 (t0) outliers start: 13 outliers final: 13 residues processed: 166 average time/residue: 0.2645 time to fit residues: 67.9547 Evaluate side-chains 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 477 SER 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 477 SER Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.090151 restraints weight = 18379.906| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.87 r_work: 0.2767 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15656 Z= 0.162 Angle : 0.467 5.111 21336 Z= 0.251 Chirality : 0.044 0.142 2484 Planarity : 0.003 0.036 2712 Dihedral : 3.963 15.309 2280 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.97 % Allowed : 8.61 % Favored : 90.41 % 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: 3.90 (0.26), residues: 320 sheet: 0.54 (0.20), residues: 748 loop : -0.73 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 274 HIS 0.002 0.001 HIS A 194 PHE 0.014 0.002 PHE D 523 TYR 0.012 0.001 TYR B 446 ARG 0.001 0.000 ARG C 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.61 seconds wall clock time: 63 minutes 41.82 seconds (3821.82 seconds total)