Starting phenix.real_space_refine on Sat Aug 23 21:18:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc8_42117/08_2025/8uc8_42117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc8_42117/08_2025/8uc8_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_42117/08_2025/8uc8_42117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc8_42117/08_2025/8uc8_42117.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc8_42117/08_2025/8uc8_42117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc8_42117/08_2025/8uc8_42117_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 9, 'PHE:plan': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 12, 'ASN:plan1': 2} 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: 3.52, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 686.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 2.67 Time building geometry restraints manager: 1.68 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: 1.170 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- 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= 0.760 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 270 TYR 0.110 0.022 TYR A 439 PHE 0.062 0.011 PHE B 109 TRP 0.184 0.035 TRP C 281 HIS 0.015 0.005 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.01297 (15152) covalent geometry : angle 1.83982 (20512) hydrogen bonds : bond 0.15155 ( 1017) hydrogen bonds : angle 7.74209 ( 3015) *********************** 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 : 0.631 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: 0.7608 (mtp) REVERT: D 369 MET cc_start: 0.8138 (ttt) cc_final: 0.7938 (ttm) REVERT: D 371 ASP cc_start: 0.7360 (t0) cc_final: 0.6801 (m-30) REVERT: D 379 MET cc_start: 0.8677 (mtp) cc_final: 0.8357 (mtm) REVERT: D 388 MET cc_start: 0.8237 (tpp) cc_final: 0.7890 (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: 0.6970 (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: 0.6628 (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: 0.7839 (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: 0.5728 time to fit residues: 222.3040 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 : 0.708 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151587 restraints weight = 15827.053| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 0.86 r_work: 0.3650 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1924 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= 0.160 Angle : 0.562 5.625 20512 Z= 0.307 Chirality : 0.043 0.153 2276 Planarity : 0.005 0.049 2604 Dihedral : 12.616 156.891 2320 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.68 % Allowed : 10.49 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1920 helix: 0.41 (0.14), residues: 1312 sheet: 1.51 (0.75), residues: 48 loop : 0.56 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 405 TYR 0.022 0.002 TYR A 411 PHE 0.015 0.001 PHE D 143 TRP 0.024 0.002 TRP D 281 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00344 (15152) covalent geometry : angle 0.56185 (20512) hydrogen bonds : bond 0.04815 ( 1017) hydrogen bonds : angle 5.24284 ( 3015) *********************** 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 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.573 Fit side-chains REVERT: D 118 LYS cc_start: 0.8007 (tptp) cc_final: 0.7769 (tttt) REVERT: D 184 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7689 (p) REVERT: D 258 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6393 (ttt180) REVERT: C 118 LYS cc_start: 0.8031 (tptp) cc_final: 0.7780 (tttt) REVERT: C 184 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7698 (p) REVERT: C 258 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6382 (ttt180) REVERT: A 118 LYS cc_start: 0.8014 (tptp) cc_final: 0.7780 (tttt) REVERT: A 184 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7718 (p) REVERT: A 258 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6416 (ttt180) REVERT: A 460 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: A 492 ARG cc_start: 0.8604 (mmp80) cc_final: 0.8217 (mmp80) REVERT: B 118 LYS cc_start: 0.8018 (tptp) cc_final: 0.7794 (tttt) REVERT: B 184 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7705 (p) REVERT: B 258 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6414 (ttt180) outliers start: 36 outliers final: 9 residues processed: 281 average time/residue: 0.5378 time to fit residues: 166.6941 Evaluate side-chains 221 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 426 ASP 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 95 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 279 HIS C 482 ASN A 482 ASN B 279 HIS B 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141709 restraints weight = 16436.831| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 0.86 r_work: 0.3545 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 15152 Z= 0.294 Angle : 0.651 8.010 20512 Z= 0.342 Chirality : 0.046 0.145 2276 Planarity : 0.005 0.047 2604 Dihedral : 11.209 131.090 2292 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.57 % Allowed : 12.35 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.18), residues: 1920 helix: 0.27 (0.13), residues: 1320 sheet: 0.94 (0.74), residues: 48 loop : -0.05 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 492 TYR 0.026 0.003 TYR D 411 PHE 0.022 0.002 PHE A 143 TRP 0.022 0.003 TRP C 281 HIS 0.007 0.002 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00682 (15152) covalent geometry : angle 0.65109 (20512) hydrogen bonds : bond 0.05064 ( 1017) hydrogen bonds : angle 5.32161 ( 3015) *********************** 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 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.580 Fit side-chains REVERT: D 113 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7715 (tpp) REVERT: D 118 LYS cc_start: 0.7984 (tptp) cc_final: 0.7694 (tttt) REVERT: D 287 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6589 (mmt) REVERT: D 482 ASN cc_start: 0.6821 (t0) cc_final: 0.6176 (t0) REVERT: C 118 LYS cc_start: 0.7999 (tptp) cc_final: 0.7732 (tttt) REVERT: C 283 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7144 (mm-30) REVERT: C 482 ASN cc_start: 0.6819 (t0) cc_final: 0.6208 (t0) REVERT: A 113 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7703 (tpp) REVERT: A 118 LYS cc_start: 0.8001 (tptp) cc_final: 0.7759 (tttt) REVERT: A 283 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7115 (mm-30) REVERT: A 287 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6559 (mmt) REVERT: A 482 ASN cc_start: 0.6812 (t0) cc_final: 0.6212 (t0) REVERT: B 118 LYS cc_start: 0.7989 (tptp) cc_final: 0.7738 (tttt) REVERT: B 287 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6586 (mmt) REVERT: B 482 ASN cc_start: 0.6829 (t0) cc_final: 0.6232 (t0) outliers start: 48 outliers final: 11 residues processed: 225 average time/residue: 0.5382 time to fit residues: 134.2135 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET 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 32 optimal weight: 0.0970 chunk 169 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 114 optimal weight: 0.0030 chunk 179 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 408 GLN C 355 HIS ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS A 408 GLN B 355 HIS B 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149914 restraints weight = 16136.241| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 0.91 r_work: 0.3597 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2917 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= 0.123 Angle : 0.492 5.931 20512 Z= 0.261 Chirality : 0.040 0.121 2276 Planarity : 0.004 0.041 2604 Dihedral : 10.033 109.868 2292 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.16 % Allowed : 15.33 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1920 helix: 0.92 (0.14), residues: 1304 sheet: 0.65 (0.69), residues: 48 loop : 0.06 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 492 TYR 0.020 0.002 TYR A 411 PHE 0.013 0.001 PHE B 236 TRP 0.023 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00265 (15152) covalent geometry : angle 0.49239 (20512) hydrogen bonds : bond 0.04049 ( 1017) hydrogen bonds : angle 4.81688 ( 3015) *********************** 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 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.521 Fit side-chains REVERT: D 118 LYS cc_start: 0.8121 (tptp) cc_final: 0.7726 (tttt) REVERT: D 192 MET cc_start: 0.7512 (mpt) cc_final: 0.7288 (mpt) REVERT: D 258 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6192 (ttt180) REVERT: D 283 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7056 (mm-30) REVERT: C 118 LYS cc_start: 0.8101 (tptp) cc_final: 0.7696 (tttt) REVERT: C 192 MET cc_start: 0.7499 (mpt) cc_final: 0.7286 (mpt) REVERT: C 258 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6222 (ttt180) REVERT: C 283 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7042 (mm-30) REVERT: C 287 MET cc_start: 0.7192 (mmt) cc_final: 0.6418 (mmt) REVERT: A 118 LYS cc_start: 0.8120 (tptp) cc_final: 0.7709 (tttt) REVERT: A 258 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6161 (ttt180) REVERT: A 283 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7023 (mm-30) REVERT: A 452 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 460 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: B 118 LYS cc_start: 0.8105 (tptp) cc_final: 0.7695 (tttt) REVERT: B 258 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6212 (ttt180) REVERT: B 283 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7053 (mm-30) REVERT: B 452 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8135 (mt-10) outliers start: 29 outliers final: 7 residues processed: 229 average time/residue: 0.5702 time to fit residues: 144.6604 Evaluate side-chains 208 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP 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 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 142 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 HIS D 355 HIS ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN C 355 HIS C 482 ASN A 279 HIS A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140452 restraints weight = 16414.403| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 0.99 r_work: 0.3521 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15152 Z= 0.294 Angle : 0.627 8.397 20512 Z= 0.325 Chirality : 0.045 0.136 2276 Planarity : 0.005 0.041 2604 Dihedral : 10.303 103.365 2292 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.98 % Allowed : 16.22 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 1920 helix: 0.59 (0.14), residues: 1300 sheet: 0.44 (0.68), residues: 48 loop : -0.26 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 267 TYR 0.026 0.002 TYR D 411 PHE 0.021 0.002 PHE B 141 TRP 0.021 0.002 TRP A 281 HIS 0.006 0.002 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00684 (15152) covalent geometry : angle 0.62728 (20512) hydrogen bonds : bond 0.04705 ( 1017) hydrogen bonds : angle 5.17166 ( 3015) *********************** 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 222 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.609 Fit side-chains REVERT: D 118 LYS cc_start: 0.8013 (tptp) cc_final: 0.7577 (tttt) REVERT: D 258 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6174 (ttt180) REVERT: D 287 MET cc_start: 0.7270 (mmt) cc_final: 0.6483 (mmt) REVERT: C 118 LYS cc_start: 0.8000 (tptp) cc_final: 0.7565 (tttt) REVERT: C 258 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6182 (ttt180) REVERT: C 287 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6478 (mmt) REVERT: A 118 LYS cc_start: 0.8022 (tptp) cc_final: 0.7581 (tttt) REVERT: A 258 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6143 (ttt180) REVERT: A 287 MET cc_start: 0.7265 (mmt) cc_final: 0.6491 (mmt) REVERT: A 452 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 118 LYS cc_start: 0.8001 (tptp) cc_final: 0.7578 (tttt) REVERT: B 258 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6167 (ttt180) REVERT: B 287 MET cc_start: 0.7266 (mmt) cc_final: 0.6490 (mmt) outliers start: 40 outliers final: 20 residues processed: 202 average time/residue: 0.5429 time to fit residues: 121.4863 Evaluate side-chains 206 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 418 MET 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 78 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 189 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 408 GLN C 482 ASN A 355 HIS A 482 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146162 restraints weight = 16083.055| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.87 r_work: 0.3577 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15152 Z= 0.144 Angle : 0.510 5.708 20512 Z= 0.268 Chirality : 0.040 0.121 2276 Planarity : 0.004 0.040 2604 Dihedral : 9.606 92.407 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.46 % Allowed : 16.89 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.19), residues: 1920 helix: 0.99 (0.14), residues: 1304 sheet: 0.52 (0.66), residues: 48 loop : -0.16 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 492 TYR 0.022 0.002 TYR D 411 PHE 0.019 0.001 PHE C 141 TRP 0.023 0.002 TRP D 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00319 (15152) covalent geometry : angle 0.50955 (20512) hydrogen bonds : bond 0.04091 ( 1017) hydrogen bonds : angle 4.82687 ( 3015) *********************** 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 234 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.457 Fit side-chains REVERT: D 118 LYS cc_start: 0.8093 (tptp) cc_final: 0.7600 (tttt) REVERT: D 258 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6115 (ttt180) REVERT: D 287 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6321 (mmt) REVERT: C 118 LYS cc_start: 0.8069 (tptp) cc_final: 0.7581 (tttt) REVERT: C 258 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6124 (ttt180) REVERT: C 283 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7060 (mm-30) REVERT: C 287 MET cc_start: 0.7148 (mmt) cc_final: 0.6338 (mmt) REVERT: A 118 LYS cc_start: 0.8093 (tptp) cc_final: 0.7600 (tttt) REVERT: A 258 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6073 (ttt180) REVERT: A 287 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6332 (mmt) REVERT: B 118 LYS cc_start: 0.8075 (tptp) cc_final: 0.7585 (tttt) REVERT: B 258 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6096 (ttt180) REVERT: B 287 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6332 (mmt) REVERT: B 452 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8177 (mt-10) outliers start: 33 outliers final: 19 residues processed: 221 average time/residue: 0.5379 time to fit residues: 131.8883 Evaluate side-chains 212 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL 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 D residue 460 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL 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 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 460 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN A 355 HIS A 429 GLN A 482 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.161705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149308 restraints weight = 16094.772| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.61 r_work: 0.3628 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15152 Z= 0.153 Angle : 0.518 5.895 20512 Z= 0.271 Chirality : 0.041 0.127 2276 Planarity : 0.004 0.041 2604 Dihedral : 9.311 83.762 2292 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.90 % Allowed : 17.04 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.19), residues: 1920 helix: 1.13 (0.14), residues: 1304 sheet: 0.47 (0.66), residues: 48 loop : -0.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 554 TYR 0.022 0.002 TYR D 411 PHE 0.015 0.001 PHE B 236 TRP 0.021 0.002 TRP D 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00343 (15152) covalent geometry : angle 0.51777 (20512) hydrogen bonds : bond 0.04019 ( 1017) hydrogen bonds : angle 4.74655 ( 3015) *********************** 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 234 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.566 Fit side-chains REVERT: D 118 LYS cc_start: 0.8060 (tptp) cc_final: 0.7555 (tttt) REVERT: D 232 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7777 (t) REVERT: D 238 ILE cc_start: 0.7545 (mp) cc_final: 0.7198 (mm) REVERT: D 258 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6117 (ttt180) REVERT: D 287 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6370 (mmt) REVERT: C 118 LYS cc_start: 0.8037 (tptp) cc_final: 0.7539 (tttt) REVERT: C 238 ILE cc_start: 0.7443 (mp) cc_final: 0.7157 (mm) REVERT: C 258 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6165 (ttt180) REVERT: C 287 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6362 (mmt) REVERT: A 118 LYS cc_start: 0.8070 (tptp) cc_final: 0.7559 (tttt) REVERT: A 232 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 258 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6071 (ttt180) REVERT: A 287 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6355 (mmt) REVERT: B 118 LYS cc_start: 0.8033 (tptp) cc_final: 0.7535 (tttt) REVERT: B 232 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (t) REVERT: B 258 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6086 (ttt180) REVERT: B 287 MET cc_start: 0.7165 (mmt) cc_final: 0.6366 (mmt) REVERT: B 452 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8120 (mt-10) outliers start: 39 outliers final: 16 residues processed: 219 average time/residue: 0.5265 time to fit residues: 128.3943 Evaluate side-chains 220 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 VAL 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 D residue 460 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 232 VAL 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 C residue 460 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 VAL 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 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 460 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 118 optimal weight: 0.0050 chunk 73 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 429 GLN C 482 ASN A 355 HIS A 429 GLN A 482 ASN B 355 HIS B 429 GLN B 482 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152807 restraints weight = 16146.326| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 0.59 r_work: 0.3677 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3327 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= 0.123 Angle : 0.492 6.207 20512 Z= 0.258 Chirality : 0.040 0.124 2276 Planarity : 0.004 0.040 2604 Dihedral : 8.888 72.164 2292 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 17.78 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1920 helix: 1.30 (0.14), residues: 1316 sheet: 0.55 (0.61), residues: 68 loop : 0.05 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 554 TYR 0.019 0.001 TYR D 411 PHE 0.028 0.001 PHE B 141 TRP 0.020 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00268 (15152) covalent geometry : angle 0.49245 (20512) hydrogen bonds : bond 0.03787 ( 1017) hydrogen bonds : angle 4.57816 ( 3015) *********************** 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 239 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.533 Fit side-chains REVERT: D 118 LYS cc_start: 0.8032 (tptp) cc_final: 0.7569 (tttt) REVERT: D 258 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6092 (ttt180) REVERT: C 118 LYS cc_start: 0.8035 (tptp) cc_final: 0.7576 (tttt) REVERT: C 258 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6102 (ttt180) REVERT: A 118 LYS cc_start: 0.8043 (tptp) cc_final: 0.7573 (tttt) REVERT: A 258 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6030 (ttt180) REVERT: A 452 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 118 LYS cc_start: 0.7995 (tptp) cc_final: 0.7555 (tttt) REVERT: B 258 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6062 (ttt180) REVERT: B 452 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8078 (mt-10) outliers start: 30 outliers final: 15 residues processed: 225 average time/residue: 0.5139 time to fit residues: 128.8352 Evaluate side-chains 212 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE 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 D residue 460 GLU Chi-restraints excluded: chain C residue 135 ILE 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 C residue 460 GLU Chi-restraints excluded: chain A residue 135 ILE 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 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 460 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 181 optimal weight: 0.4980 chunk 173 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 118 optimal weight: 0.0060 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150655 restraints weight = 16318.845| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 0.79 r_work: 0.3591 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15152 Z= 0.125 Angle : 0.504 7.497 20512 Z= 0.263 Chirality : 0.040 0.134 2276 Planarity : 0.004 0.042 2604 Dihedral : 8.655 59.799 2292 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.93 % Allowed : 18.53 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1920 helix: 1.37 (0.14), residues: 1316 sheet: 0.59 (0.60), residues: 68 loop : 0.07 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 554 TYR 0.019 0.001 TYR A 411 PHE 0.017 0.001 PHE B 236 TRP 0.029 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00270 (15152) covalent geometry : angle 0.50405 (20512) hydrogen bonds : bond 0.03705 ( 1017) hydrogen bonds : angle 4.52337 ( 3015) *********************** 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 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.438 Fit side-chains REVERT: D 118 LYS cc_start: 0.7988 (tptp) cc_final: 0.7521 (tttt) REVERT: D 258 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6034 (ttt180) REVERT: C 118 LYS cc_start: 0.7973 (tptp) cc_final: 0.7521 (tttt) REVERT: C 258 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.6058 (ttt180) REVERT: A 118 LYS cc_start: 0.7996 (tptp) cc_final: 0.7540 (tttt) REVERT: A 258 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6022 (ttt180) REVERT: B 118 LYS cc_start: 0.7938 (tptp) cc_final: 0.7504 (tttt) REVERT: B 258 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.6037 (ttt180) REVERT: B 452 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 26 outliers final: 10 residues processed: 213 average time/residue: 0.5734 time to fit residues: 135.3000 Evaluate side-chains 206 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 460 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 127 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151101 restraints weight = 16254.168| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 0.72 r_work: 0.3607 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15152 Z= 0.139 Angle : 0.515 8.571 20512 Z= 0.268 Chirality : 0.040 0.133 2276 Planarity : 0.004 0.041 2604 Dihedral : 8.432 58.619 2292 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.34 % Allowed : 19.27 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1920 helix: 1.39 (0.14), residues: 1316 sheet: 0.45 (0.62), residues: 48 loop : 0.05 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 554 TYR 0.020 0.002 TYR D 411 PHE 0.017 0.001 PHE A 236 TRP 0.023 0.002 TRP A 281 HIS 0.005 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00310 (15152) covalent geometry : angle 0.51532 (20512) hydrogen bonds : bond 0.03778 ( 1017) hydrogen bonds : angle 4.52411 ( 3015) ********************** 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 210 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.593 Fit side-chains REVERT: D 118 LYS cc_start: 0.8093 (tptp) cc_final: 0.7593 (tttt) REVERT: D 238 ILE cc_start: 0.7539 (mp) cc_final: 0.7211 (mm) REVERT: D 258 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6149 (ttt180) REVERT: C 118 LYS cc_start: 0.8116 (tptp) cc_final: 0.7612 (tttt) REVERT: C 238 ILE cc_start: 0.7526 (mp) cc_final: 0.7210 (mm) REVERT: C 258 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6182 (ttt180) REVERT: A 118 LYS cc_start: 0.8124 (tptp) cc_final: 0.7624 (tttt) REVERT: A 238 ILE cc_start: 0.7487 (mp) cc_final: 0.7212 (mm) REVERT: A 258 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6155 (ttt180) REVERT: B 118 LYS cc_start: 0.8065 (tptp) cc_final: 0.7580 (tttt) REVERT: B 238 ILE cc_start: 0.7488 (mp) cc_final: 0.7187 (mm) REVERT: B 258 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6136 (ttt180) REVERT: B 452 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8185 (mt-10) outliers start: 18 outliers final: 11 residues processed: 202 average time/residue: 0.5431 time to fit residues: 121.5060 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 460 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 482 ASN A 482 ASN B 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.164017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149551 restraints weight = 16232.925| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 0.90 r_work: 0.3605 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3471 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= 0.136 Angle : 0.521 9.188 20512 Z= 0.269 Chirality : 0.040 0.127 2276 Planarity : 0.004 0.040 2604 Dihedral : 8.299 59.207 2292 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.19 % Allowed : 19.20 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 1920 helix: 1.39 (0.14), residues: 1320 sheet: 0.51 (0.62), residues: 48 loop : 0.07 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 554 TYR 0.020 0.002 TYR B 411 PHE 0.026 0.001 PHE C 236 TRP 0.023 0.002 TRP A 281 HIS 0.005 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00302 (15152) covalent geometry : angle 0.52131 (20512) hydrogen bonds : bond 0.03723 ( 1017) hydrogen bonds : angle 4.52476 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4505.31 seconds wall clock time: 77 minutes 47.99 seconds (4667.99 seconds total)