Starting phenix.real_space_refine on Tue Dec 31 04:19:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc8_42117/12_2024/8uc8_42117_neut.cif" } resolution = 3.0 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9720 2.51 5 N 2460 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14804 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 174 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Restraints were copied for chains: B, C, D Time building chain proxies: 8.47, per 1000 atoms: 0.57 Number of scatterers: 14804 At special positions: 0 Unit cell: (121.656, 121.656, 112.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2516 8.00 N 2460 7.00 C 9720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 70.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 removed outlier: 4.093A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 584 Processing helix chain 'C' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 194 removed outlier: 4.076A pdb=" N PHE C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.019A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.719A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.767A pdb=" N SER B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.021A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 584 Processing sheet with id=AA1, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.588A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.483A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 3015 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: 4.47 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2276 1.27 - 1.41: 3900 1.41 - 1.54: 8520 1.54 - 1.68: 268 1.68 - 1.82: 188 Bond restraints: 15152 Sorted by residual: bond pdb=" C ARG C 404 " pdb=" O ARG C 404 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.22e-02 6.72e+03 6.29e+01 bond pdb=" C ARG A 404 " pdb=" O ARG A 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.26e+01 bond pdb=" C ARG B 404 " pdb=" O ARG B 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.22e+01 bond pdb=" C ARG D 404 " pdb=" O ARG D 404 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.17e+01 bond pdb=" C11 PCW C 902 " pdb=" O3 PCW C 902 " ideal model delta sigma weight residual 1.326 1.466 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 20359 5.18 - 10.35: 133 10.35 - 15.53: 8 15.53 - 20.70: 8 20.70 - 25.88: 4 Bond angle restraints: 20512 Sorted by residual: angle pdb=" C19 PCW A 705 " pdb=" C20 PCW A 705 " pdb=" C21 PCW A 705 " ideal model delta sigma weight residual 127.82 153.70 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C19 PCW B 901 " pdb=" C20 PCW B 901 " pdb=" C21 PCW B 901 " ideal model delta sigma weight residual 127.82 153.70 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " pdb=" C21 PCW A 704 " ideal model delta sigma weight residual 127.82 153.69 -25.87 3.00e+00 1.11e-01 7.43e+01 angle pdb=" C19 PCW C 901 " pdb=" C20 PCW C 901 " pdb=" C21 PCW C 901 " ideal model delta sigma weight residual 127.82 153.67 -25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" C38 PCW B 902 " pdb=" C39 PCW B 902 " pdb=" C40 PCW B 902 " ideal model delta sigma weight residual 127.57 148.22 -20.65 3.00e+00 1.11e-01 4.74e+01 ... (remaining 20507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 8736 35.48 - 70.96: 164 70.96 - 106.45: 12 106.45 - 141.93: 0 141.93 - 177.41: 4 Dihedral angle restraints: 8916 sinusoidal: 3212 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR C 361 " pdb=" C TYR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 361 " pdb=" C TYR B 361 " pdb=" N GLY B 362 " pdb=" CA GLY B 362 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 8913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1464 0.075 - 0.150: 601 0.150 - 0.225: 167 0.225 - 0.300: 36 0.300 - 0.375: 8 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA TRP C 281 " pdb=" N TRP C 281 " pdb=" C TRP C 281 " pdb=" CB TRP C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA TRP A 281 " pdb=" N TRP A 281 " pdb=" C TRP A 281 " pdb=" CB TRP A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TRP D 281 " pdb=" N TRP D 281 " pdb=" C TRP D 281 " pdb=" CB TRP D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 2273 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " 0.184 2.00e-02 2.50e+03 8.90e-02 1.98e+02 pdb=" CG TRP C 281 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " 0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.184 2.00e-02 2.50e+03 8.89e-02 1.98e+02 pdb=" CG TRP A 281 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 281 " 0.184 2.00e-02 2.50e+03 8.89e-02 1.98e+02 pdb=" CG TRP D 281 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 281 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP D 281 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP D 281 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP D 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 281 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 281 " 0.110 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 281 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP D 281 " 0.079 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 417 2.74 - 3.28: 15831 3.28 - 3.82: 24744 3.82 - 4.36: 31799 4.36 - 4.90: 53479 Nonbonded interactions: 126270 Sorted by model distance: nonbonded pdb=" NH1 ARG B 142 " pdb=" OD1 ASP B 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG D 142 " pdb=" OD1 ASP D 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG C 142 " pdb=" OD1 ASP C 146 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG A 142 " pdb=" OD1 ASP A 146 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG C 438 " pdb=" OE2 GLU C 446 " model vdw 2.257 3.120 ... (remaining 126265 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' and (resid 94 through 586 or (resid 701 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 702 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 703 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'B' and (resid 94 through 586 or (resid 901 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 902 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 903 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'C' and (resid 94 through 586 or (resid 901 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 902 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 903 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'D' and (resid 94 through 586 or (resid 701 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 702 and (name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22)) or (res \ id 703 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.490 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 0.013 0.140 15152 Z= 0.855 Angle : 1.840 25.880 20512 Z= 1.194 Chirality : 0.089 0.375 2276 Planarity : 0.014 0.089 2604 Dihedral : 15.096 177.408 5228 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.60 % Allowed : 3.87 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.18), residues: 1920 helix: -1.21 (0.12), residues: 1288 sheet: 0.84 (0.75), residues: 48 loop : 0.14 (0.29), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.184 0.035 TRP C 281 HIS 0.015 0.005 HIS C 310 PHE 0.062 0.011 PHE B 109 TYR 0.110 0.022 TYR A 439 ARG 0.009 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 344 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.7185 (tptp) cc_final: 0.6708 (tttt) REVERT: D 140 ASP cc_start: 0.6825 (m-30) cc_final: 0.6568 (m-30) REVERT: D 152 MET cc_start: 0.7554 (tpp) cc_final: 0.7291 (tpt) REVERT: D 283 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5692 (mm-30) REVERT: D 305 MET cc_start: 0.7991 (mtp) cc_final: 0.7609 (mtp) REVERT: D 371 ASP cc_start: 0.7360 (t0) cc_final: 0.6802 (m-30) REVERT: D 388 MET cc_start: 0.8237 (tpp) cc_final: 0.7889 (mmm) REVERT: D 412 LYS cc_start: 0.7240 (mttp) cc_final: 0.6995 (mtmm) REVERT: D 429 GLN cc_start: 0.7091 (tp40) cc_final: 0.6627 (tp40) REVERT: D 433 ASP cc_start: 0.7418 (m-30) cc_final: 0.6909 (m-30) REVERT: D 446 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6774 (tt0) REVERT: D 448 ASN cc_start: 0.6817 (t0) cc_final: 0.6258 (m-40) REVERT: D 459 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6762 (tt0) REVERT: D 460 GLU cc_start: 0.7749 (tt0) cc_final: 0.7513 (pt0) REVERT: D 482 ASN cc_start: 0.6463 (p0) cc_final: 0.5994 (t0) REVERT: D 492 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6971 (mmp80) REVERT: C 118 LYS cc_start: 0.7182 (tptp) cc_final: 0.6729 (tttt) REVERT: C 140 ASP cc_start: 0.6821 (m-30) cc_final: 0.6558 (m-30) REVERT: C 152 MET cc_start: 0.7552 (tpp) cc_final: 0.7350 (tpt) REVERT: C 283 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5784 (mm-30) REVERT: C 305 MET cc_start: 0.8006 (mtp) cc_final: 0.7638 (mtp) REVERT: C 371 ASP cc_start: 0.7355 (t0) cc_final: 0.6793 (m-30) REVERT: C 412 LYS cc_start: 0.7274 (mttp) cc_final: 0.7023 (mtmm) REVERT: C 429 GLN cc_start: 0.7106 (tp40) cc_final: 0.6421 (tp-100) REVERT: C 433 ASP cc_start: 0.7405 (m-30) cc_final: 0.6782 (m-30) REVERT: C 446 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6797 (tt0) REVERT: C 448 ASN cc_start: 0.6861 (t0) cc_final: 0.6306 (m-40) REVERT: C 459 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6758 (tt0) REVERT: C 460 GLU cc_start: 0.7759 (tt0) cc_final: 0.7517 (pt0) REVERT: C 482 ASN cc_start: 0.6433 (p0) cc_final: 0.5998 (t0) REVERT: C 492 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.6981 (mmp80) REVERT: A 118 LYS cc_start: 0.7179 (tptp) cc_final: 0.6707 (tttt) REVERT: A 140 ASP cc_start: 0.6840 (m-30) cc_final: 0.6573 (m-30) REVERT: A 152 MET cc_start: 0.7557 (tpp) cc_final: 0.7334 (tpt) REVERT: A 283 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5671 (mm-30) REVERT: A 305 MET cc_start: 0.7948 (mtp) cc_final: 0.7565 (mtp) REVERT: A 369 MET cc_start: 0.8229 (ttt) cc_final: 0.8006 (ttm) REVERT: A 371 ASP cc_start: 0.7336 (t0) cc_final: 0.6791 (m-30) REVERT: A 388 MET cc_start: 0.8230 (tpp) cc_final: 0.7856 (mmm) REVERT: A 412 LYS cc_start: 0.7235 (mttp) cc_final: 0.7007 (mtmm) REVERT: A 429 GLN cc_start: 0.7067 (tp40) cc_final: 0.6627 (tp40) REVERT: A 433 ASP cc_start: 0.7327 (m-30) cc_final: 0.6880 (m-30) REVERT: A 446 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6810 (tt0) REVERT: A 448 ASN cc_start: 0.6857 (t0) cc_final: 0.6273 (m-40) REVERT: A 459 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6748 (tt0) REVERT: A 482 ASN cc_start: 0.6382 (p0) cc_final: 0.5966 (t0) REVERT: B 118 LYS cc_start: 0.7203 (tptp) cc_final: 0.6753 (tttt) REVERT: B 140 ASP cc_start: 0.6831 (m-30) cc_final: 0.6562 (m-30) REVERT: B 152 MET cc_start: 0.7532 (tpp) cc_final: 0.7320 (tpt) REVERT: B 283 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5767 (mm-30) REVERT: B 305 MET cc_start: 0.7969 (mtp) cc_final: 0.7595 (mtp) REVERT: B 371 ASP cc_start: 0.7339 (t0) cc_final: 0.6778 (m-30) REVERT: B 388 MET cc_start: 0.8187 (tpp) cc_final: 0.7840 (mmm) REVERT: B 412 LYS cc_start: 0.7279 (mttp) cc_final: 0.7024 (mtmm) REVERT: B 429 GLN cc_start: 0.7095 (tp40) cc_final: 0.6612 (tp40) REVERT: B 433 ASP cc_start: 0.7386 (m-30) cc_final: 0.6954 (m-30) REVERT: B 446 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6770 (tt0) REVERT: B 448 ASN cc_start: 0.6870 (t0) cc_final: 0.6278 (m-40) REVERT: B 459 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6761 (tt0) REVERT: B 460 GLU cc_start: 0.7789 (tt0) cc_final: 0.7579 (pt0) REVERT: B 482 ASN cc_start: 0.6358 (p0) cc_final: 0.5974 (t0) REVERT: B 492 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6981 (mmp80) outliers start: 8 outliers final: 7 residues processed: 352 average time/residue: 1.2176 time to fit residues: 473.0576 Evaluate side-chains 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 404 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN D 323 GLN C 103 GLN C 323 GLN A 103 GLN A 323 GLN A 416 GLN B 103 GLN B 323 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.220 Angle : 0.564 5.280 20512 Z= 0.307 Chirality : 0.043 0.157 2276 Planarity : 0.005 0.051 2604 Dihedral : 12.502 154.036 2320 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.75 % Allowed : 10.34 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1920 helix: 0.48 (0.14), residues: 1288 sheet: 1.65 (0.75), residues: 48 loop : 0.55 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 281 HIS 0.003 0.001 HIS C 421 PHE 0.015 0.001 PHE D 143 TYR 0.020 0.002 TYR A 411 ARG 0.006 0.001 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: D 118 LYS cc_start: 0.6884 (tptp) cc_final: 0.6453 (tttt) REVERT: D 140 ASP cc_start: 0.6997 (m-30) cc_final: 0.6710 (m-30) REVERT: D 184 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6542 (p) REVERT: D 258 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5250 (ttt180) REVERT: D 285 PHE cc_start: 0.6888 (m-10) cc_final: 0.6661 (m-10) REVERT: D 287 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6214 (mmm) REVERT: D 371 ASP cc_start: 0.6967 (t0) cc_final: 0.6588 (m-30) REVERT: D 412 LYS cc_start: 0.7390 (mttp) cc_final: 0.7165 (mttp) REVERT: D 429 GLN cc_start: 0.7008 (tp40) cc_final: 0.6378 (tp40) REVERT: D 433 ASP cc_start: 0.7389 (m-30) cc_final: 0.6880 (m-30) REVERT: D 446 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6762 (tt0) REVERT: D 448 ASN cc_start: 0.7058 (t0) cc_final: 0.6436 (m-40) REVERT: D 460 GLU cc_start: 0.7636 (tt0) cc_final: 0.7059 (mt-10) REVERT: D 492 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7229 (mmp80) REVERT: C 118 LYS cc_start: 0.6882 (tptp) cc_final: 0.6459 (tttt) REVERT: C 140 ASP cc_start: 0.6927 (m-30) cc_final: 0.6691 (m-30) REVERT: C 184 THR cc_start: 0.7092 (OUTLIER) cc_final: 0.6547 (p) REVERT: C 258 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.5194 (ttt180) REVERT: C 287 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6192 (mmm) REVERT: C 371 ASP cc_start: 0.6956 (t0) cc_final: 0.6566 (m-30) REVERT: C 429 GLN cc_start: 0.7010 (tp40) cc_final: 0.6307 (tp-100) REVERT: C 433 ASP cc_start: 0.7380 (m-30) cc_final: 0.6803 (m-30) REVERT: C 446 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6814 (tt0) REVERT: C 448 ASN cc_start: 0.7041 (t0) cc_final: 0.6395 (m-40) REVERT: C 452 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 460 GLU cc_start: 0.7651 (tt0) cc_final: 0.7241 (pt0) REVERT: C 492 ARG cc_start: 0.7427 (mmt-90) cc_final: 0.7227 (mmp80) REVERT: A 118 LYS cc_start: 0.6877 (tptp) cc_final: 0.6455 (tttt) REVERT: A 140 ASP cc_start: 0.6993 (m-30) cc_final: 0.6702 (m-30) REVERT: A 184 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6549 (p) REVERT: A 258 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.5258 (ttt180) REVERT: A 285 PHE cc_start: 0.6894 (m-10) cc_final: 0.6674 (m-10) REVERT: A 371 ASP cc_start: 0.6959 (t0) cc_final: 0.6587 (m-30) REVERT: A 412 LYS cc_start: 0.7375 (mttp) cc_final: 0.7151 (mttp) REVERT: A 429 GLN cc_start: 0.6955 (tp40) cc_final: 0.6359 (tp40) REVERT: A 433 ASP cc_start: 0.7383 (m-30) cc_final: 0.6901 (m-30) REVERT: A 446 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6802 (tt0) REVERT: A 448 ASN cc_start: 0.7036 (t0) cc_final: 0.6406 (m-40) REVERT: A 460 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: B 118 LYS cc_start: 0.6882 (tptp) cc_final: 0.6461 (tttt) REVERT: B 140 ASP cc_start: 0.6919 (m-30) cc_final: 0.6667 (m-30) REVERT: B 184 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6550 (p) REVERT: B 238 ILE cc_start: 0.6635 (mp) cc_final: 0.6425 (mm) REVERT: B 258 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.5250 (ttt180) REVERT: B 285 PHE cc_start: 0.6906 (m-10) cc_final: 0.6672 (m-10) REVERT: B 371 ASP cc_start: 0.6948 (t0) cc_final: 0.6569 (m-30) REVERT: B 412 LYS cc_start: 0.7388 (mttp) cc_final: 0.7179 (mttp) REVERT: B 429 GLN cc_start: 0.7003 (tp40) cc_final: 0.6237 (tp-100) REVERT: B 433 ASP cc_start: 0.7378 (m-30) cc_final: 0.6809 (m-30) REVERT: B 446 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6768 (tt0) REVERT: B 448 ASN cc_start: 0.7055 (t0) cc_final: 0.6423 (m-40) REVERT: B 460 GLU cc_start: 0.7656 (tt0) cc_final: 0.7272 (pt0) outliers start: 37 outliers final: 8 residues processed: 278 average time/residue: 1.2861 time to fit residues: 393.4969 Evaluate side-chains 253 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 chunk 188 optimal weight: 0.0670 chunk 155 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.201 Angle : 0.505 5.287 20512 Z= 0.271 Chirality : 0.041 0.129 2276 Planarity : 0.004 0.049 2604 Dihedral : 10.923 132.305 2292 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.93 % Allowed : 12.50 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1920 helix: 0.88 (0.14), residues: 1308 sheet: 1.05 (0.69), residues: 48 loop : 0.32 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 281 HIS 0.005 0.001 HIS C 421 PHE 0.014 0.001 PHE C 143 TYR 0.022 0.002 TYR A 411 ARG 0.005 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 1.703 Fit side-chains REVERT: D 118 LYS cc_start: 0.6977 (tptp) cc_final: 0.6458 (tttt) REVERT: D 140 ASP cc_start: 0.7032 (m-30) cc_final: 0.6716 (m-30) REVERT: D 152 MET cc_start: 0.7202 (ttm) cc_final: 0.6916 (ttm) REVERT: D 184 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6438 (p) REVERT: D 283 GLU cc_start: 0.6633 (mt-10) cc_final: 0.5612 (mm-30) REVERT: D 285 PHE cc_start: 0.6830 (m-10) cc_final: 0.6594 (m-10) REVERT: D 287 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5687 (mmm) REVERT: D 371 ASP cc_start: 0.6952 (t0) cc_final: 0.6589 (m-30) REVERT: D 433 ASP cc_start: 0.7672 (m-30) cc_final: 0.7249 (m-30) REVERT: D 446 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6677 (tt0) REVERT: D 448 ASN cc_start: 0.7129 (t0) cc_final: 0.6416 (m-40) REVERT: D 460 GLU cc_start: 0.7758 (tt0) cc_final: 0.7114 (pt0) REVERT: D 482 ASN cc_start: 0.6570 (t0) cc_final: 0.5855 (t0) REVERT: D 492 ARG cc_start: 0.7533 (mmt-90) cc_final: 0.7213 (mmp80) REVERT: C 118 LYS cc_start: 0.6949 (tptp) cc_final: 0.6452 (tttt) REVERT: C 140 ASP cc_start: 0.7027 (m-30) cc_final: 0.6708 (m-30) REVERT: C 152 MET cc_start: 0.7192 (ttm) cc_final: 0.6908 (ttm) REVERT: C 184 THR cc_start: 0.6926 (OUTLIER) cc_final: 0.6413 (p) REVERT: C 283 GLU cc_start: 0.6637 (mt-10) cc_final: 0.5619 (mm-30) REVERT: C 287 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5674 (mmm) REVERT: C 371 ASP cc_start: 0.6950 (t0) cc_final: 0.6573 (m-30) REVERT: C 433 ASP cc_start: 0.7664 (m-30) cc_final: 0.7228 (m-30) REVERT: C 446 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6725 (tt0) REVERT: C 448 ASN cc_start: 0.7090 (t0) cc_final: 0.6391 (m-40) REVERT: C 452 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 460 GLU cc_start: 0.7783 (tt0) cc_final: 0.7147 (pt0) REVERT: C 492 ARG cc_start: 0.7567 (mmt-90) cc_final: 0.7257 (mmp80) REVERT: A 118 LYS cc_start: 0.6977 (tptp) cc_final: 0.6464 (tttt) REVERT: A 140 ASP cc_start: 0.7026 (m-30) cc_final: 0.6714 (m-30) REVERT: A 184 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.6411 (p) REVERT: A 238 ILE cc_start: 0.6691 (mm) cc_final: 0.6486 (mm) REVERT: A 283 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6027 (pt0) REVERT: A 285 PHE cc_start: 0.6829 (m-10) cc_final: 0.6576 (m-10) REVERT: A 371 ASP cc_start: 0.6958 (t0) cc_final: 0.6604 (m-30) REVERT: A 429 GLN cc_start: 0.7104 (tp40) cc_final: 0.6319 (tp-100) REVERT: A 433 ASP cc_start: 0.7556 (m-30) cc_final: 0.6922 (m-30) REVERT: A 446 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6704 (tt0) REVERT: A 448 ASN cc_start: 0.7104 (t0) cc_final: 0.6385 (m-40) REVERT: A 452 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 482 ASN cc_start: 0.6580 (t0) cc_final: 0.5902 (t0) REVERT: A 492 ARG cc_start: 0.7969 (mmp80) cc_final: 0.7513 (mmp80) REVERT: B 118 LYS cc_start: 0.6978 (tptp) cc_final: 0.6485 (tttt) REVERT: B 140 ASP cc_start: 0.6990 (m-30) cc_final: 0.6673 (m-30) REVERT: B 184 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6415 (p) REVERT: B 283 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5638 (mm-30) REVERT: B 285 PHE cc_start: 0.6837 (m-10) cc_final: 0.6603 (m-10) REVERT: B 371 ASP cc_start: 0.6941 (t0) cc_final: 0.6581 (m-30) REVERT: B 433 ASP cc_start: 0.7665 (m-30) cc_final: 0.7243 (m-30) REVERT: B 446 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6687 (tt0) REVERT: B 448 ASN cc_start: 0.7132 (t0) cc_final: 0.6391 (m-40) REVERT: B 460 GLU cc_start: 0.7757 (tt0) cc_final: 0.7104 (pt0) REVERT: B 492 ARG cc_start: 0.7921 (mmp80) cc_final: 0.7335 (mmp80) outliers start: 26 outliers final: 8 residues processed: 264 average time/residue: 1.2381 time to fit residues: 362.3139 Evaluate side-chains 247 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 90 optimal weight: 30.0000 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 0.0060 chunk 50 optimal weight: 5.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 GLN C 408 GLN C 482 ASN A 408 GLN B 408 GLN B 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15152 Z= 0.145 Angle : 0.457 4.890 20512 Z= 0.243 Chirality : 0.039 0.118 2276 Planarity : 0.004 0.052 2604 Dihedral : 9.378 108.071 2292 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.46 % Allowed : 13.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.19), residues: 1920 helix: 1.21 (0.14), residues: 1312 sheet: 0.89 (0.68), residues: 48 loop : 0.41 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.026 0.001 PHE B 141 TYR 0.019 0.001 TYR C 411 ARG 0.006 0.001 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.642 Fit side-chains REVERT: D 118 LYS cc_start: 0.6964 (tptp) cc_final: 0.6363 (tttt) REVERT: D 140 ASP cc_start: 0.7070 (m-30) cc_final: 0.6821 (m-30) REVERT: D 184 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6794 (p) REVERT: D 258 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.5021 (ttt180) REVERT: D 285 PHE cc_start: 0.6636 (m-10) cc_final: 0.6290 (m-10) REVERT: D 369 MET cc_start: 0.8037 (ttm) cc_final: 0.7728 (ttt) REVERT: D 371 ASP cc_start: 0.7025 (t0) cc_final: 0.6729 (m-30) REVERT: D 429 GLN cc_start: 0.7077 (tp40) cc_final: 0.6276 (tp-100) REVERT: D 433 ASP cc_start: 0.7622 (m-30) cc_final: 0.7044 (m-30) REVERT: D 446 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6645 (tt0) REVERT: D 448 ASN cc_start: 0.7022 (t0) cc_final: 0.6445 (m110) REVERT: D 460 GLU cc_start: 0.7621 (tt0) cc_final: 0.6982 (mt-10) REVERT: D 492 ARG cc_start: 0.7542 (mmt-90) cc_final: 0.7197 (mmp80) REVERT: D 494 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 118 LYS cc_start: 0.6963 (tptp) cc_final: 0.6447 (tttt) REVERT: C 140 ASP cc_start: 0.7071 (m-30) cc_final: 0.6813 (m-30) REVERT: C 184 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6578 (p) REVERT: C 258 ARG cc_start: 0.5309 (OUTLIER) cc_final: 0.5094 (ttt180) REVERT: C 287 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5595 (mmm) REVERT: C 369 MET cc_start: 0.8032 (ttm) cc_final: 0.7722 (ttt) REVERT: C 371 ASP cc_start: 0.7017 (t0) cc_final: 0.6710 (m-30) REVERT: C 433 ASP cc_start: 0.7618 (m-30) cc_final: 0.7242 (m-30) REVERT: C 446 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6710 (tt0) REVERT: C 448 ASN cc_start: 0.7123 (t0) cc_final: 0.6443 (m110) REVERT: C 452 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 460 GLU cc_start: 0.7779 (tt0) cc_final: 0.7133 (mt-10) REVERT: C 492 ARG cc_start: 0.7543 (mmt-90) cc_final: 0.7201 (mmp80) REVERT: C 494 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 118 LYS cc_start: 0.6962 (tptp) cc_final: 0.6366 (tttt) REVERT: A 140 ASP cc_start: 0.7119 (m-30) cc_final: 0.6867 (m-30) REVERT: A 184 THR cc_start: 0.7013 (OUTLIER) cc_final: 0.6568 (p) REVERT: A 258 ARG cc_start: 0.5275 (OUTLIER) cc_final: 0.5072 (ttt180) REVERT: A 285 PHE cc_start: 0.6637 (m-10) cc_final: 0.6293 (m-10) REVERT: A 287 MET cc_start: 0.5804 (mmt) cc_final: 0.4995 (mmt) REVERT: A 371 ASP cc_start: 0.7040 (t0) cc_final: 0.6746 (m-30) REVERT: A 429 GLN cc_start: 0.7076 (tp40) cc_final: 0.6293 (tp-100) REVERT: A 433 ASP cc_start: 0.7509 (m-30) cc_final: 0.6943 (m-30) REVERT: A 446 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6611 (tt0) REVERT: A 448 ASN cc_start: 0.7046 (t0) cc_final: 0.6434 (m110) REVERT: A 452 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 492 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7377 (mmp80) REVERT: A 494 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 118 LYS cc_start: 0.6967 (tptp) cc_final: 0.6452 (tttt) REVERT: B 140 ASP cc_start: 0.6814 (m-30) cc_final: 0.6572 (m-30) REVERT: B 184 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6560 (p) REVERT: B 258 ARG cc_start: 0.5297 (OUTLIER) cc_final: 0.5087 (ttt180) REVERT: B 283 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5969 (pt0) REVERT: B 285 PHE cc_start: 0.6597 (m-10) cc_final: 0.6238 (m-10) REVERT: B 287 MET cc_start: 0.5804 (mmt) cc_final: 0.4984 (mmt) REVERT: B 369 MET cc_start: 0.8040 (ttm) cc_final: 0.7728 (ttt) REVERT: B 371 ASP cc_start: 0.7014 (t0) cc_final: 0.6718 (m-30) REVERT: B 433 ASP cc_start: 0.7626 (m-30) cc_final: 0.7224 (m-30) REVERT: B 446 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6654 (tt0) REVERT: B 448 ASN cc_start: 0.7007 (t0) cc_final: 0.6434 (m110) REVERT: B 460 GLU cc_start: 0.7732 (tt0) cc_final: 0.7095 (mt-10) REVERT: B 492 ARG cc_start: 0.7979 (mmp80) cc_final: 0.7389 (mmp80) REVERT: B 494 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7669 (mt-10) outliers start: 33 outliers final: 8 residues processed: 281 average time/residue: 1.1526 time to fit residues: 360.5871 Evaluate side-chains 256 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.210 Angle : 0.499 5.081 20512 Z= 0.261 Chirality : 0.040 0.130 2276 Planarity : 0.004 0.054 2604 Dihedral : 8.890 97.328 2292 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.60 % Allowed : 15.70 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.19), residues: 1920 helix: 1.26 (0.14), residues: 1316 sheet: 0.35 (0.66), residues: 48 loop : 0.29 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 281 HIS 0.006 0.001 HIS D 421 PHE 0.014 0.001 PHE C 143 TYR 0.023 0.002 TYR D 411 ARG 0.004 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 1.742 Fit side-chains REVERT: D 118 LYS cc_start: 0.6943 (tptp) cc_final: 0.6328 (tttt) REVERT: D 121 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: D 140 ASP cc_start: 0.7112 (m-30) cc_final: 0.6837 (m-30) REVERT: D 192 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6205 (mpt) REVERT: D 258 ARG cc_start: 0.5289 (OUTLIER) cc_final: 0.5036 (ttt180) REVERT: D 283 GLU cc_start: 0.6477 (mt-10) cc_final: 0.5981 (pt0) REVERT: D 285 PHE cc_start: 0.6597 (m-10) cc_final: 0.6309 (m-10) REVERT: D 371 ASP cc_start: 0.7171 (t0) cc_final: 0.6808 (m-30) REVERT: D 433 ASP cc_start: 0.7717 (m-30) cc_final: 0.7204 (m-30) REVERT: D 446 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6702 (tt0) REVERT: D 448 ASN cc_start: 0.7036 (t0) cc_final: 0.6358 (m110) REVERT: D 482 ASN cc_start: 0.6660 (t0) cc_final: 0.6043 (t0) REVERT: D 492 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.7289 (mmp80) REVERT: C 118 LYS cc_start: 0.6942 (tptp) cc_final: 0.6331 (tttt) REVERT: C 140 ASP cc_start: 0.7111 (m-30) cc_final: 0.6830 (m-30) REVERT: C 192 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6117 (mpt) REVERT: C 258 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.5037 (ttt180) REVERT: C 283 GLU cc_start: 0.6489 (mt-10) cc_final: 0.5993 (pt0) REVERT: C 371 ASP cc_start: 0.7167 (t0) cc_final: 0.6796 (m-30) REVERT: C 433 ASP cc_start: 0.7709 (m-30) cc_final: 0.7188 (m-30) REVERT: C 446 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6739 (tt0) REVERT: C 448 ASN cc_start: 0.7172 (t0) cc_final: 0.6479 (m110) REVERT: C 452 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7668 (mt-10) REVERT: C 482 ASN cc_start: 0.6511 (t0) cc_final: 0.5993 (t0) REVERT: C 492 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7268 (mmp80) REVERT: C 494 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 118 LYS cc_start: 0.6941 (tptp) cc_final: 0.6332 (tttt) REVERT: A 121 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: A 140 ASP cc_start: 0.7105 (m-30) cc_final: 0.6837 (m-30) REVERT: A 192 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6198 (mpt) REVERT: A 258 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.5033 (ttt180) REVERT: A 283 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5947 (pt0) REVERT: A 285 PHE cc_start: 0.6594 (m-10) cc_final: 0.6304 (m-10) REVERT: A 287 MET cc_start: 0.5885 (mmt) cc_final: 0.5072 (mmt) REVERT: A 371 ASP cc_start: 0.7184 (t0) cc_final: 0.6818 (m-30) REVERT: A 433 ASP cc_start: 0.7703 (m-30) cc_final: 0.7220 (m-30) REVERT: A 446 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6728 (tt0) REVERT: A 448 ASN cc_start: 0.7139 (t0) cc_final: 0.6414 (m110) REVERT: A 452 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 482 ASN cc_start: 0.6702 (t0) cc_final: 0.5987 (t0) REVERT: A 492 ARG cc_start: 0.8065 (mmp80) cc_final: 0.7760 (mmp80) REVERT: B 118 LYS cc_start: 0.6945 (tptp) cc_final: 0.6337 (tttt) REVERT: B 121 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: B 135 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7318 (tt) REVERT: B 140 ASP cc_start: 0.6924 (m-30) cc_final: 0.6597 (m-30) REVERT: B 192 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6228 (mpt) REVERT: B 258 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.5039 (ttt180) REVERT: B 283 GLU cc_start: 0.6497 (mt-10) cc_final: 0.5944 (pt0) REVERT: B 285 PHE cc_start: 0.6628 (m-10) cc_final: 0.6339 (m-10) REVERT: B 287 MET cc_start: 0.5895 (mmt) cc_final: 0.5087 (mmt) REVERT: B 371 ASP cc_start: 0.7168 (t0) cc_final: 0.6800 (m-30) REVERT: B 433 ASP cc_start: 0.7714 (m-30) cc_final: 0.7212 (m-30) REVERT: B 446 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6650 (tt0) REVERT: B 448 ASN cc_start: 0.7032 (t0) cc_final: 0.6489 (m110) REVERT: B 482 ASN cc_start: 0.6576 (t0) cc_final: 0.6008 (t0) REVERT: B 492 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7705 (mmp80) REVERT: B 494 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7766 (mt-10) outliers start: 35 outliers final: 13 residues processed: 253 average time/residue: 1.2098 time to fit residues: 339.7719 Evaluate side-chains 260 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS C 355 HIS A 355 HIS B 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.210 Angle : 0.490 4.893 20512 Z= 0.256 Chirality : 0.040 0.124 2276 Planarity : 0.004 0.052 2604 Dihedral : 8.563 86.106 2292 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.57 % Allowed : 15.25 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.19), residues: 1920 helix: 1.32 (0.14), residues: 1312 sheet: 0.50 (0.62), residues: 68 loop : 0.26 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 281 HIS 0.005 0.001 HIS C 421 PHE 0.027 0.001 PHE A 141 TYR 0.022 0.002 TYR D 411 ARG 0.004 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 2.072 Fit side-chains REVERT: D 118 LYS cc_start: 0.6960 (tptp) cc_final: 0.6278 (tttt) REVERT: D 140 ASP cc_start: 0.6974 (m-30) cc_final: 0.6708 (m-30) REVERT: D 192 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6044 (mpt) REVERT: D 258 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.5004 (ttt180) REVERT: D 283 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5952 (pt0) REVERT: D 285 PHE cc_start: 0.6564 (m-10) cc_final: 0.6261 (m-10) REVERT: D 287 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5148 (mmt) REVERT: D 371 ASP cc_start: 0.7180 (t0) cc_final: 0.6819 (m-30) REVERT: D 433 ASP cc_start: 0.7715 (m-30) cc_final: 0.7201 (m-30) REVERT: D 446 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6730 (tt0) REVERT: D 448 ASN cc_start: 0.7099 (t0) cc_final: 0.6544 (m110) REVERT: D 492 ARG cc_start: 0.7789 (mmt-90) cc_final: 0.7383 (mmp80) REVERT: C 118 LYS cc_start: 0.6945 (tptp) cc_final: 0.6247 (tttt) REVERT: C 140 ASP cc_start: 0.7109 (m-30) cc_final: 0.6859 (m-30) REVERT: C 192 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6200 (mpt) REVERT: C 258 ARG cc_start: 0.5297 (OUTLIER) cc_final: 0.5005 (ttt180) REVERT: C 283 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5975 (pt0) REVERT: C 371 ASP cc_start: 0.7175 (t0) cc_final: 0.6819 (m-30) REVERT: C 433 ASP cc_start: 0.7706 (m-30) cc_final: 0.7170 (m-30) REVERT: C 446 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6827 (tt0) REVERT: C 448 ASN cc_start: 0.7083 (t0) cc_final: 0.6403 (m110) REVERT: C 452 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 492 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7351 (mmp80) REVERT: A 118 LYS cc_start: 0.6959 (tptp) cc_final: 0.6278 (tttt) REVERT: A 140 ASP cc_start: 0.6982 (m-30) cc_final: 0.6715 (m-30) REVERT: A 192 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6044 (mpt) REVERT: A 258 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.5007 (ttt180) REVERT: A 283 GLU cc_start: 0.6504 (mt-10) cc_final: 0.5953 (pt0) REVERT: A 285 PHE cc_start: 0.6566 (m-10) cc_final: 0.6263 (m-10) REVERT: A 287 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5083 (mmt) REVERT: A 371 ASP cc_start: 0.7186 (t0) cc_final: 0.6825 (m-30) REVERT: A 433 ASP cc_start: 0.7707 (m-30) cc_final: 0.7176 (m-30) REVERT: A 446 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6768 (tt0) REVERT: A 448 ASN cc_start: 0.7039 (t0) cc_final: 0.6416 (m110) REVERT: A 452 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 492 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7744 (mmp80) REVERT: B 118 LYS cc_start: 0.6960 (tptp) cc_final: 0.6282 (tttt) REVERT: B 121 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: B 135 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7318 (tt) REVERT: B 140 ASP cc_start: 0.7001 (m-30) cc_final: 0.6732 (m-30) REVERT: B 192 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6225 (mpt) REVERT: B 258 ARG cc_start: 0.5295 (OUTLIER) cc_final: 0.5005 (ttt180) REVERT: B 283 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5949 (pt0) REVERT: B 285 PHE cc_start: 0.6581 (m-10) cc_final: 0.6276 (m-10) REVERT: B 287 MET cc_start: 0.5903 (mmt) cc_final: 0.5079 (mmt) REVERT: B 371 ASP cc_start: 0.7171 (t0) cc_final: 0.6808 (m-30) REVERT: B 433 ASP cc_start: 0.7716 (m-30) cc_final: 0.7173 (m-30) REVERT: B 446 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6801 (tt0) REVERT: B 448 ASN cc_start: 0.7107 (t0) cc_final: 0.6525 (m110) REVERT: B 492 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7777 (mmp80) outliers start: 48 outliers final: 17 residues processed: 259 average time/residue: 1.1609 time to fit residues: 336.4704 Evaluate side-chains 257 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 0.0000 chunk 114 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 355 HIS C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.170 Angle : 0.480 4.859 20512 Z= 0.251 Chirality : 0.039 0.115 2276 Planarity : 0.004 0.050 2604 Dihedral : 8.198 76.412 2292 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.38 % Allowed : 15.62 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.19), residues: 1920 helix: 1.45 (0.14), residues: 1316 sheet: 0.59 (0.60), residues: 68 loop : 0.37 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 281 HIS 0.004 0.001 HIS D 421 PHE 0.027 0.001 PHE C 141 TYR 0.020 0.001 TYR D 411 ARG 0.004 0.000 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.846 Fit side-chains REVERT: D 118 LYS cc_start: 0.6949 (tptp) cc_final: 0.6254 (tttt) REVERT: D 140 ASP cc_start: 0.7069 (m-30) cc_final: 0.6787 (m-30) REVERT: D 192 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6006 (mpt) REVERT: D 238 ILE cc_start: 0.6409 (mp) cc_final: 0.6204 (mm) REVERT: D 258 ARG cc_start: 0.5277 (OUTLIER) cc_final: 0.4984 (ttt180) REVERT: D 283 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5975 (pt0) REVERT: D 285 PHE cc_start: 0.6553 (m-10) cc_final: 0.6246 (m-10) REVERT: D 371 ASP cc_start: 0.7122 (t0) cc_final: 0.6765 (m-30) REVERT: D 433 ASP cc_start: 0.7704 (m-30) cc_final: 0.7235 (m-30) REVERT: D 446 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6706 (tt0) REVERT: D 448 ASN cc_start: 0.7021 (t0) cc_final: 0.6468 (m110) REVERT: D 482 ASN cc_start: 0.6274 (t0) cc_final: 0.5771 (t0) REVERT: D 492 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7304 (mmp80) REVERT: D 494 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 118 LYS cc_start: 0.6942 (tptp) cc_final: 0.6228 (tttt) REVERT: C 140 ASP cc_start: 0.7004 (m-30) cc_final: 0.6713 (m-30) REVERT: C 192 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5968 (mpt) REVERT: C 238 ILE cc_start: 0.6569 (mm) cc_final: 0.6366 (mm) REVERT: C 258 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.4991 (ttt180) REVERT: C 283 GLU cc_start: 0.6438 (mt-10) cc_final: 0.5935 (pt0) REVERT: C 287 MET cc_start: 0.5827 (mmt) cc_final: 0.5036 (mmt) REVERT: C 371 ASP cc_start: 0.7130 (t0) cc_final: 0.6773 (m-30) REVERT: C 433 ASP cc_start: 0.7699 (m-30) cc_final: 0.7179 (m-30) REVERT: C 446 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6858 (tt0) REVERT: C 448 ASN cc_start: 0.7062 (t0) cc_final: 0.6389 (m110) REVERT: C 452 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7867 (mt-10) REVERT: C 482 ASN cc_start: 0.6328 (t0) cc_final: 0.5869 (t0) REVERT: C 492 ARG cc_start: 0.7768 (mmt-90) cc_final: 0.7290 (mmp80) REVERT: C 494 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 118 LYS cc_start: 0.6949 (tptp) cc_final: 0.6257 (tttt) REVERT: A 140 ASP cc_start: 0.7035 (m-30) cc_final: 0.6774 (m-30) REVERT: A 192 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6008 (mpt) REVERT: A 238 ILE cc_start: 0.6547 (mm) cc_final: 0.6323 (mm) REVERT: A 258 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.5002 (ttt180) REVERT: A 283 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5939 (pt0) REVERT: A 285 PHE cc_start: 0.6557 (m-10) cc_final: 0.6248 (m-10) REVERT: A 287 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.4972 (mmt) REVERT: A 371 ASP cc_start: 0.7129 (t0) cc_final: 0.6772 (m-30) REVERT: A 433 ASP cc_start: 0.7650 (m-30) cc_final: 0.7161 (m-30) REVERT: A 446 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6782 (tt0) REVERT: A 448 ASN cc_start: 0.7023 (t0) cc_final: 0.6299 (m110) REVERT: A 452 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 482 ASN cc_start: 0.6468 (t0) cc_final: 0.5963 (t0) REVERT: A 492 ARG cc_start: 0.8036 (mmp80) cc_final: 0.7675 (mmp80) REVERT: A 494 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 118 LYS cc_start: 0.6960 (tptp) cc_final: 0.6285 (tttt) REVERT: B 140 ASP cc_start: 0.7003 (m-30) cc_final: 0.6706 (m-30) REVERT: B 258 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4993 (ttt180) REVERT: B 283 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5936 (pt0) REVERT: B 285 PHE cc_start: 0.6565 (m-10) cc_final: 0.6254 (m-10) REVERT: B 287 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.4969 (mmt) REVERT: B 371 ASP cc_start: 0.7085 (t0) cc_final: 0.6760 (m-30) REVERT: B 433 ASP cc_start: 0.7666 (m-30) cc_final: 0.7162 (m-30) REVERT: B 446 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6786 (tt0) REVERT: B 448 ASN cc_start: 0.7001 (t0) cc_final: 0.6493 (m110) REVERT: B 482 ASN cc_start: 0.6542 (t0) cc_final: 0.6070 (t0) REVERT: B 492 ARG cc_start: 0.8039 (mmp80) cc_final: 0.7691 (mmp80) REVERT: B 494 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 32 outliers final: 13 residues processed: 248 average time/residue: 1.2263 time to fit residues: 338.3333 Evaluate side-chains 252 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 168 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN C 355 HIS A 156 ASN B 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.178 Angle : 0.482 5.305 20512 Z= 0.251 Chirality : 0.039 0.116 2276 Planarity : 0.004 0.049 2604 Dihedral : 8.043 69.700 2292 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.01 % Allowed : 16.00 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.19), residues: 1920 helix: 1.49 (0.14), residues: 1316 sheet: 0.48 (0.66), residues: 48 loop : 0.33 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 281 HIS 0.004 0.001 HIS D 421 PHE 0.019 0.001 PHE C 141 TYR 0.020 0.001 TYR D 411 ARG 0.005 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 2.169 Fit side-chains REVERT: D 118 LYS cc_start: 0.6919 (tptp) cc_final: 0.6212 (tttt) REVERT: D 140 ASP cc_start: 0.7030 (m-30) cc_final: 0.6751 (m-30) REVERT: D 192 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5997 (mpt) REVERT: D 238 ILE cc_start: 0.6541 (mp) cc_final: 0.6335 (mm) REVERT: D 258 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.4985 (ttt180) REVERT: D 283 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5946 (pt0) REVERT: D 285 PHE cc_start: 0.6551 (m-10) cc_final: 0.6245 (m-10) REVERT: D 287 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5094 (mmm) REVERT: D 369 MET cc_start: 0.7707 (ttm) cc_final: 0.7374 (ttt) REVERT: D 371 ASP cc_start: 0.7108 (t0) cc_final: 0.6770 (m-30) REVERT: D 433 ASP cc_start: 0.7706 (m-30) cc_final: 0.7210 (m-30) REVERT: D 446 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6811 (tt0) REVERT: D 448 ASN cc_start: 0.7029 (t0) cc_final: 0.6477 (m110) REVERT: D 492 ARG cc_start: 0.7791 (mmt-90) cc_final: 0.7344 (mmp80) REVERT: C 118 LYS cc_start: 0.6914 (tptp) cc_final: 0.6214 (tttt) REVERT: C 121 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: C 140 ASP cc_start: 0.7057 (m-30) cc_final: 0.6789 (m-30) REVERT: C 175 TRP cc_start: 0.7398 (t-100) cc_final: 0.6796 (m100) REVERT: C 192 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6023 (mpt) REVERT: C 238 ILE cc_start: 0.6712 (mm) cc_final: 0.6505 (mm) REVERT: C 258 ARG cc_start: 0.5307 (OUTLIER) cc_final: 0.4982 (ttt180) REVERT: C 283 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5981 (pt0) REVERT: C 371 ASP cc_start: 0.7062 (t0) cc_final: 0.6748 (m-30) REVERT: C 433 ASP cc_start: 0.7698 (m-30) cc_final: 0.7177 (m-30) REVERT: C 446 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6942 (tt0) REVERT: C 448 ASN cc_start: 0.7066 (t0) cc_final: 0.6398 (m110) REVERT: C 452 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 492 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7280 (mmp80) REVERT: C 494 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 118 LYS cc_start: 0.6935 (tptp) cc_final: 0.6254 (tttt) REVERT: A 140 ASP cc_start: 0.7083 (m-30) cc_final: 0.6814 (m-30) REVERT: A 175 TRP cc_start: 0.7406 (t-100) cc_final: 0.6787 (m100) REVERT: A 192 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5994 (mpt) REVERT: A 238 ILE cc_start: 0.6777 (mm) cc_final: 0.6576 (mm) REVERT: A 258 ARG cc_start: 0.5300 (OUTLIER) cc_final: 0.4989 (ttt180) REVERT: A 283 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5948 (pt0) REVERT: A 285 PHE cc_start: 0.6559 (m-10) cc_final: 0.6251 (m-10) REVERT: A 287 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.4982 (mmt) REVERT: A 371 ASP cc_start: 0.7105 (t0) cc_final: 0.6772 (m-30) REVERT: A 433 ASP cc_start: 0.7700 (m-30) cc_final: 0.7203 (m-30) REVERT: A 448 ASN cc_start: 0.7029 (t0) cc_final: 0.6305 (m110) REVERT: A 452 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 492 ARG cc_start: 0.8038 (mmp80) cc_final: 0.7669 (mmp80) REVERT: A 494 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 118 LYS cc_start: 0.6936 (tptp) cc_final: 0.6314 (tttt) REVERT: B 140 ASP cc_start: 0.6990 (m-30) cc_final: 0.6712 (m-30) REVERT: B 175 TRP cc_start: 0.7386 (t-100) cc_final: 0.6770 (m100) REVERT: B 258 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4983 (ttt180) REVERT: B 283 GLU cc_start: 0.6452 (mt-10) cc_final: 0.5939 (pt0) REVERT: B 285 PHE cc_start: 0.6566 (m-10) cc_final: 0.6256 (m-10) REVERT: B 287 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.4984 (mmt) REVERT: B 369 MET cc_start: 0.7709 (ttm) cc_final: 0.7373 (ttt) REVERT: B 371 ASP cc_start: 0.7102 (t0) cc_final: 0.6760 (m-30) REVERT: B 433 ASP cc_start: 0.7708 (m-30) cc_final: 0.7195 (m-30) REVERT: B 446 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6837 (tt0) REVERT: B 448 ASN cc_start: 0.7005 (t0) cc_final: 0.6457 (m110) REVERT: B 492 ARG cc_start: 0.8040 (mmp80) cc_final: 0.7686 (mmp80) REVERT: B 494 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7755 (mt-10) outliers start: 27 outliers final: 8 residues processed: 246 average time/residue: 1.2703 time to fit residues: 346.6202 Evaluate side-chains 252 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.211 Angle : 0.502 6.412 20512 Z= 0.260 Chirality : 0.040 0.116 2276 Planarity : 0.004 0.048 2604 Dihedral : 8.079 65.852 2292 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.08 % Allowed : 15.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.19), residues: 1920 helix: 1.46 (0.14), residues: 1312 sheet: 0.39 (0.65), residues: 48 loop : 0.29 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 281 HIS 0.005 0.001 HIS C 421 PHE 0.018 0.001 PHE C 141 TYR 0.021 0.002 TYR D 411 ARG 0.005 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 1.845 Fit side-chains REVERT: D 118 LYS cc_start: 0.6894 (tptp) cc_final: 0.6138 (tttt) REVERT: D 140 ASP cc_start: 0.7038 (m-30) cc_final: 0.6771 (m-30) REVERT: D 192 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6083 (mpt) REVERT: D 238 ILE cc_start: 0.6639 (mp) cc_final: 0.6425 (mm) REVERT: D 258 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.4994 (ttt180) REVERT: D 283 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5960 (pt0) REVERT: D 285 PHE cc_start: 0.6562 (m-10) cc_final: 0.6255 (m-10) REVERT: D 287 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5151 (mmm) REVERT: D 371 ASP cc_start: 0.7134 (t0) cc_final: 0.6778 (m-30) REVERT: D 433 ASP cc_start: 0.7710 (m-30) cc_final: 0.7165 (m-30) REVERT: D 446 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6818 (tt0) REVERT: D 448 ASN cc_start: 0.7009 (t0) cc_final: 0.6382 (m110) REVERT: D 492 ARG cc_start: 0.7830 (mmt-90) cc_final: 0.7289 (mmp80) REVERT: C 118 LYS cc_start: 0.6886 (tptp) cc_final: 0.6140 (tttt) REVERT: C 121 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: C 140 ASP cc_start: 0.7021 (m-30) cc_final: 0.6761 (m-30) REVERT: C 192 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6062 (mpt) REVERT: C 238 ILE cc_start: 0.6682 (mm) cc_final: 0.6475 (mm) REVERT: C 258 ARG cc_start: 0.5310 (OUTLIER) cc_final: 0.4996 (ttt180) REVERT: C 283 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5957 (pt0) REVERT: C 287 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5210 (mmm) REVERT: C 371 ASP cc_start: 0.7138 (t0) cc_final: 0.6782 (m-30) REVERT: C 433 ASP cc_start: 0.7704 (m-30) cc_final: 0.7158 (m-30) REVERT: C 448 ASN cc_start: 0.7085 (t0) cc_final: 0.6423 (m110) REVERT: C 452 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 482 ASN cc_start: 0.6305 (t0) cc_final: 0.5856 (t0) REVERT: C 492 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7323 (mmp80) REVERT: A 118 LYS cc_start: 0.6895 (tptp) cc_final: 0.6140 (tttt) REVERT: A 140 ASP cc_start: 0.7046 (m-30) cc_final: 0.6809 (m-30) REVERT: A 192 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6077 (mpt) REVERT: A 258 ARG cc_start: 0.5295 (OUTLIER) cc_final: 0.4986 (ttt180) REVERT: A 283 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6001 (pt0) REVERT: A 285 PHE cc_start: 0.6574 (m-10) cc_final: 0.6258 (m-10) REVERT: A 371 ASP cc_start: 0.7127 (t0) cc_final: 0.6783 (m-30) REVERT: A 433 ASP cc_start: 0.7699 (m-30) cc_final: 0.7156 (m-30) REVERT: A 448 ASN cc_start: 0.7040 (t0) cc_final: 0.6350 (m-40) REVERT: A 452 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 492 ARG cc_start: 0.8043 (mmp80) cc_final: 0.7732 (mmp80) REVERT: B 118 LYS cc_start: 0.6902 (tptp) cc_final: 0.6236 (tttt) REVERT: B 140 ASP cc_start: 0.7059 (m-30) cc_final: 0.6717 (m-30) REVERT: B 192 MET cc_start: 0.6719 (mpt) cc_final: 0.6292 (mpt) REVERT: B 258 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4998 (ttt180) REVERT: B 283 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6005 (pt0) REVERT: B 285 PHE cc_start: 0.6582 (m-10) cc_final: 0.6266 (m-10) REVERT: B 371 ASP cc_start: 0.7129 (t0) cc_final: 0.6771 (m-30) REVERT: B 433 ASP cc_start: 0.7713 (m-30) cc_final: 0.7159 (m-30) REVERT: B 446 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6928 (tt0) REVERT: B 448 ASN cc_start: 0.7037 (t0) cc_final: 0.6483 (m110) REVERT: B 482 ASN cc_start: 0.6265 (t0) cc_final: 0.5809 (t0) REVERT: B 492 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7747 (mmp80) outliers start: 28 outliers final: 8 residues processed: 238 average time/residue: 1.2265 time to fit residues: 325.3319 Evaluate side-chains 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 176 optimal weight: 0.0060 chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 355 HIS A 355 HIS A 482 ASN B 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.186 Angle : 0.501 8.435 20512 Z= 0.258 Chirality : 0.039 0.116 2276 Planarity : 0.004 0.048 2604 Dihedral : 7.975 60.785 2292 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.49 % Allowed : 16.59 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.19), residues: 1920 helix: 1.50 (0.14), residues: 1312 sheet: 0.51 (0.64), residues: 48 loop : 0.34 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 281 HIS 0.004 0.001 HIS C 421 PHE 0.019 0.001 PHE C 141 TYR 0.020 0.001 TYR B 411 ARG 0.005 0.000 ARG C 554 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 1.771 Fit side-chains REVERT: D 118 LYS cc_start: 0.7005 (tptp) cc_final: 0.6248 (tttt) REVERT: D 121 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: D 140 ASP cc_start: 0.7091 (m-30) cc_final: 0.6823 (m-30) REVERT: D 192 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6063 (mpt) REVERT: D 258 ARG cc_start: 0.5289 (OUTLIER) cc_final: 0.4978 (ttt180) REVERT: D 283 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5949 (pt0) REVERT: D 285 PHE cc_start: 0.6536 (m-10) cc_final: 0.6220 (m-10) REVERT: D 287 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.5115 (mmm) REVERT: D 369 MET cc_start: 0.7652 (ttm) cc_final: 0.7308 (ttt) REVERT: D 371 ASP cc_start: 0.7108 (t0) cc_final: 0.6760 (m-30) REVERT: D 433 ASP cc_start: 0.7700 (m-30) cc_final: 0.7188 (m-30) REVERT: D 446 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6692 (tt0) REVERT: D 448 ASN cc_start: 0.7002 (t0) cc_final: 0.6380 (m110) REVERT: D 492 ARG cc_start: 0.7858 (mmt-90) cc_final: 0.7360 (mmp80) REVERT: C 118 LYS cc_start: 0.6931 (tptp) cc_final: 0.6207 (tttt) REVERT: C 121 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: C 140 ASP cc_start: 0.7064 (m-30) cc_final: 0.6820 (m-30) REVERT: C 192 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6008 (mpt) REVERT: C 258 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4978 (ttt180) REVERT: C 283 GLU cc_start: 0.6446 (mt-10) cc_final: 0.5945 (pt0) REVERT: C 287 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5223 (mmm) REVERT: C 369 MET cc_start: 0.7645 (ttm) cc_final: 0.7300 (ttt) REVERT: C 371 ASP cc_start: 0.7107 (t0) cc_final: 0.6759 (m-30) REVERT: C 433 ASP cc_start: 0.7694 (m-30) cc_final: 0.7164 (m-30) REVERT: C 448 ASN cc_start: 0.7087 (t0) cc_final: 0.6401 (m110) REVERT: C 452 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 492 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7323 (mmp80) REVERT: A 118 LYS cc_start: 0.7005 (tptp) cc_final: 0.6249 (tttt) REVERT: A 121 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: A 140 ASP cc_start: 0.7043 (m-30) cc_final: 0.6810 (m-30) REVERT: A 192 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6058 (mpt) REVERT: A 283 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5991 (pt0) REVERT: A 285 PHE cc_start: 0.6545 (m-10) cc_final: 0.6224 (m-10) REVERT: A 371 ASP cc_start: 0.7152 (t0) cc_final: 0.6784 (m-30) REVERT: A 433 ASP cc_start: 0.7691 (m-30) cc_final: 0.7189 (m-30) REVERT: A 446 GLU cc_start: 0.7249 (tt0) cc_final: 0.6901 (mm-30) REVERT: A 448 ASN cc_start: 0.7035 (t0) cc_final: 0.6343 (m-40) REVERT: A 452 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 492 ARG cc_start: 0.8040 (mmp80) cc_final: 0.7735 (mmp80) REVERT: B 118 LYS cc_start: 0.6941 (tptp) cc_final: 0.6203 (tttt) REVERT: B 121 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: B 140 ASP cc_start: 0.6992 (m-30) cc_final: 0.6666 (m-30) REVERT: B 258 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.4983 (ttt180) REVERT: B 283 GLU cc_start: 0.6470 (mt-10) cc_final: 0.5990 (pt0) REVERT: B 285 PHE cc_start: 0.6551 (m-10) cc_final: 0.6230 (m-10) REVERT: B 369 MET cc_start: 0.7655 (ttm) cc_final: 0.7312 (ttt) REVERT: B 371 ASP cc_start: 0.7100 (t0) cc_final: 0.6750 (m-30) REVERT: B 433 ASP cc_start: 0.7705 (m-30) cc_final: 0.7182 (m-30) REVERT: B 446 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6957 (tt0) REVERT: B 448 ASN cc_start: 0.7026 (t0) cc_final: 0.6472 (m110) REVERT: B 492 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7687 (mmp80) REVERT: B 494 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7755 (mt-10) outliers start: 20 outliers final: 5 residues processed: 236 average time/residue: 1.2488 time to fit residues: 326.3164 Evaluate side-chains 245 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 355 HIS C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152380 restraints weight = 16077.011| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 0.98 r_work: 0.3657 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.179 Angle : 0.501 9.682 20512 Z= 0.258 Chirality : 0.039 0.122 2276 Planarity : 0.004 0.048 2604 Dihedral : 7.879 59.002 2292 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.56 % Allowed : 16.52 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.19), residues: 1920 helix: 1.53 (0.14), residues: 1312 sheet: 0.53 (0.64), residues: 48 loop : 0.35 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 281 HIS 0.004 0.001 HIS C 421 PHE 0.019 0.001 PHE C 141 TYR 0.020 0.001 TYR D 411 ARG 0.005 0.000 ARG C 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.44 seconds wall clock time: 101 minutes 14.29 seconds (6074.29 seconds total)