Starting phenix.real_space_refine on Fri May 16 18:49:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc8_42117/05_2025/8uc8_42117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc8_42117/05_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_42117/05_2025/8uc8_42117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc8_42117/05_2025/8uc8_42117.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc8_42117/05_2025/8uc8_42117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc8_42117/05_2025/8uc8_42117_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9720 2.51 5 N 2460 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14804 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3630 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 174 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'PCW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 32 Restraints were copied for chains: B, C, D Time building chain proxies: 8.52, per 1000 atoms: 0.58 Number of scatterers: 14804 At special positions: 0 Unit cell: (121.656, 121.656, 112.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2516 8.00 N 2460 7.00 C 9720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.0 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 70.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 removed outlier: 4.093A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 103 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 584 Processing helix chain 'C' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 194 removed outlier: 4.076A pdb=" N PHE C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.019A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.719A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.165A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.766A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.020A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.093A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 194 removed outlier: 4.077A pdb=" N PHE B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.573A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.151A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.720A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.166A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.767A pdb=" N SER B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.021A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 584 Processing sheet with id=AA1, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.589A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.484A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.588A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.483A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 4.32 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.120 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.030 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 1920 helix: -1.21 (0.12), residues: 1288 sheet: 0.84 (0.75), residues: 48 loop : 0.14 (0.29), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.184 0.035 TRP C 281 HIS 0.015 0.005 HIS C 310 PHE 0.062 0.011 PHE B 109 TYR 0.110 0.022 TYR A 439 ARG 0.009 0.001 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.15155 ( 1017) hydrogen bonds : angle 7.74209 ( 3015) covalent geometry : bond 0.01297 (15152) covalent geometry : angle 1.83982 (20512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 344 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.7185 (tptp) cc_final: 0.6708 (tttt) REVERT: D 140 ASP cc_start: 0.6825 (m-30) cc_final: 0.6568 (m-30) REVERT: D 152 MET cc_start: 0.7554 (tpp) cc_final: 0.7291 (tpt) REVERT: D 283 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5692 (mm-30) REVERT: D 305 MET cc_start: 0.7991 (mtp) cc_final: 0.7609 (mtp) REVERT: D 371 ASP cc_start: 0.7360 (t0) cc_final: 0.6802 (m-30) REVERT: D 388 MET cc_start: 0.8237 (tpp) cc_final: 0.7889 (mmm) REVERT: D 412 LYS cc_start: 0.7240 (mttp) cc_final: 0.6995 (mtmm) REVERT: D 429 GLN cc_start: 0.7091 (tp40) cc_final: 0.6627 (tp40) REVERT: D 433 ASP cc_start: 0.7418 (m-30) cc_final: 0.6909 (m-30) REVERT: D 446 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6774 (tt0) REVERT: D 448 ASN cc_start: 0.6817 (t0) cc_final: 0.6258 (m-40) REVERT: D 459 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6762 (tt0) REVERT: D 460 GLU cc_start: 0.7749 (tt0) cc_final: 0.7513 (pt0) REVERT: D 482 ASN cc_start: 0.6463 (p0) cc_final: 0.5994 (t0) REVERT: D 492 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6971 (mmp80) REVERT: C 118 LYS cc_start: 0.7182 (tptp) cc_final: 0.6729 (tttt) REVERT: C 140 ASP cc_start: 0.6821 (m-30) cc_final: 0.6558 (m-30) REVERT: C 152 MET cc_start: 0.7552 (tpp) cc_final: 0.7350 (tpt) REVERT: C 283 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5784 (mm-30) REVERT: C 305 MET cc_start: 0.8006 (mtp) cc_final: 0.7638 (mtp) REVERT: C 371 ASP cc_start: 0.7355 (t0) cc_final: 0.6793 (m-30) REVERT: C 412 LYS cc_start: 0.7274 (mttp) cc_final: 0.7023 (mtmm) REVERT: C 429 GLN cc_start: 0.7106 (tp40) cc_final: 0.6421 (tp-100) REVERT: C 433 ASP cc_start: 0.7405 (m-30) cc_final: 0.6782 (m-30) REVERT: C 446 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6797 (tt0) REVERT: C 448 ASN cc_start: 0.6861 (t0) cc_final: 0.6306 (m-40) REVERT: C 459 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6758 (tt0) REVERT: C 460 GLU cc_start: 0.7759 (tt0) cc_final: 0.7517 (pt0) REVERT: C 482 ASN cc_start: 0.6433 (p0) cc_final: 0.5998 (t0) REVERT: C 492 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.6981 (mmp80) REVERT: A 118 LYS cc_start: 0.7179 (tptp) cc_final: 0.6707 (tttt) REVERT: A 140 ASP cc_start: 0.6840 (m-30) cc_final: 0.6573 (m-30) REVERT: A 152 MET cc_start: 0.7557 (tpp) cc_final: 0.7334 (tpt) REVERT: A 283 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5671 (mm-30) REVERT: A 305 MET cc_start: 0.7948 (mtp) cc_final: 0.7565 (mtp) REVERT: A 369 MET cc_start: 0.8229 (ttt) cc_final: 0.8006 (ttm) REVERT: A 371 ASP cc_start: 0.7336 (t0) cc_final: 0.6791 (m-30) REVERT: A 388 MET cc_start: 0.8230 (tpp) cc_final: 0.7856 (mmm) REVERT: A 412 LYS cc_start: 0.7235 (mttp) cc_final: 0.7007 (mtmm) REVERT: A 429 GLN cc_start: 0.7067 (tp40) cc_final: 0.6627 (tp40) REVERT: A 433 ASP cc_start: 0.7327 (m-30) cc_final: 0.6880 (m-30) REVERT: A 446 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6810 (tt0) REVERT: A 448 ASN cc_start: 0.6857 (t0) cc_final: 0.6273 (m-40) REVERT: A 459 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6748 (tt0) REVERT: A 482 ASN cc_start: 0.6382 (p0) cc_final: 0.5966 (t0) REVERT: B 118 LYS cc_start: 0.7203 (tptp) cc_final: 0.6753 (tttt) REVERT: B 140 ASP cc_start: 0.6831 (m-30) cc_final: 0.6562 (m-30) REVERT: B 152 MET cc_start: 0.7532 (tpp) cc_final: 0.7320 (tpt) REVERT: B 283 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5767 (mm-30) REVERT: B 305 MET cc_start: 0.7969 (mtp) cc_final: 0.7595 (mtp) REVERT: B 371 ASP cc_start: 0.7339 (t0) cc_final: 0.6778 (m-30) REVERT: B 388 MET cc_start: 0.8187 (tpp) cc_final: 0.7840 (mmm) REVERT: B 412 LYS cc_start: 0.7279 (mttp) cc_final: 0.7024 (mtmm) REVERT: B 429 GLN cc_start: 0.7095 (tp40) cc_final: 0.6612 (tp40) REVERT: B 433 ASP cc_start: 0.7386 (m-30) cc_final: 0.6954 (m-30) REVERT: B 446 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6770 (tt0) REVERT: B 448 ASN cc_start: 0.6870 (t0) cc_final: 0.6278 (m-40) REVERT: B 459 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6761 (tt0) REVERT: B 460 GLU cc_start: 0.7789 (tt0) cc_final: 0.7579 (pt0) REVERT: B 482 ASN cc_start: 0.6358 (p0) cc_final: 0.5974 (t0) REVERT: B 492 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6981 (mmp80) outliers start: 8 outliers final: 7 residues processed: 352 average time/residue: 1.1202 time to fit residues: 436.5230 Evaluate side-chains 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 404 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN D 323 GLN C 103 GLN C 323 GLN A 103 GLN A 323 GLN A 416 GLN B 103 GLN B 323 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154845 restraints weight = 15811.162| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.60 r_work: 0.3656 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.160 Angle : 0.564 5.280 20512 Z= 0.307 Chirality : 0.043 0.157 2276 Planarity : 0.005 0.051 2604 Dihedral : 12.502 154.036 2320 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.75 % Allowed : 10.34 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1920 helix: 0.48 (0.14), residues: 1288 sheet: 1.65 (0.75), residues: 48 loop : 0.55 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 281 HIS 0.003 0.001 HIS C 421 PHE 0.015 0.001 PHE D 143 TYR 0.020 0.002 TYR A 411 ARG 0.006 0.001 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 1017) hydrogen bonds : angle 5.23326 ( 3015) covalent geometry : bond 0.00342 (15152) covalent geometry : angle 0.56407 (20512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: D 118 LYS cc_start: 0.8108 (tptp) cc_final: 0.7856 (tttt) REVERT: D 184 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 258 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6465 (ttt180) REVERT: D 287 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7532 (mmm) REVERT: D 401 ASP cc_start: 0.7844 (p0) cc_final: 0.7626 (p0) REVERT: D 460 GLU cc_start: 0.8540 (tt0) cc_final: 0.8295 (mt-10) REVERT: C 118 LYS cc_start: 0.8101 (tptp) cc_final: 0.7867 (tttt) REVERT: C 184 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 258 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6431 (ttt180) REVERT: C 287 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7524 (mmm) REVERT: A 118 LYS cc_start: 0.8123 (tptp) cc_final: 0.7869 (tttt) REVERT: A 184 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 258 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6488 (ttt180) REVERT: A 460 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: B 118 LYS cc_start: 0.8098 (tptp) cc_final: 0.7877 (tttt) REVERT: B 184 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7772 (p) REVERT: B 238 ILE cc_start: 0.7569 (mp) cc_final: 0.7291 (mm) REVERT: B 258 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6491 (ttt180) outliers start: 37 outliers final: 8 residues processed: 278 average time/residue: 1.2081 time to fit residues: 370.8014 Evaluate side-chains 215 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 150 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150321 restraints weight = 16000.105| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 0.88 r_work: 0.3622 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2546 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= 0.142 Angle : 0.510 5.292 20512 Z= 0.273 Chirality : 0.041 0.126 2276 Planarity : 0.004 0.049 2604 Dihedral : 11.024 134.913 2292 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.38 % Allowed : 13.39 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 1920 helix: 0.87 (0.14), residues: 1308 sheet: 1.06 (0.71), residues: 48 loop : 0.34 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 281 HIS 0.005 0.001 HIS C 421 PHE 0.015 0.001 PHE D 236 TYR 0.023 0.002 TYR B 411 ARG 0.005 0.001 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1017) hydrogen bonds : angle 4.89208 ( 3015) covalent geometry : bond 0.00308 (15152) covalent geometry : angle 0.51011 (20512) *********************** 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 251 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.736 Fit side-chains REVERT: D 118 LYS cc_start: 0.8115 (tptp) cc_final: 0.7772 (tttt) REVERT: D 184 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7604 (p) REVERT: D 287 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7022 (mmm) REVERT: D 482 ASN cc_start: 0.6705 (t0) cc_final: 0.5974 (t0) REVERT: D 492 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8374 (mmp80) REVERT: C 118 LYS cc_start: 0.8076 (tptp) cc_final: 0.7746 (tttt) REVERT: C 184 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 283 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6875 (mm-30) REVERT: C 287 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7035 (mmm) REVERT: C 482 ASN cc_start: 0.6704 (t0) cc_final: 0.6016 (t0) REVERT: C 492 ARG cc_start: 0.8657 (mmp80) cc_final: 0.8336 (mmp80) REVERT: A 118 LYS cc_start: 0.8092 (tptp) cc_final: 0.7763 (tttt) REVERT: A 184 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7627 (p) REVERT: A 452 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 482 ASN cc_start: 0.6828 (t0) cc_final: 0.6164 (t0) REVERT: A 492 ARG cc_start: 0.8675 (mmp80) cc_final: 0.8396 (mmp80) REVERT: B 118 LYS cc_start: 0.8071 (tptp) cc_final: 0.7776 (tttt) REVERT: B 184 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7635 (p) REVERT: B 283 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6835 (mm-30) REVERT: B 452 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8057 (mt-10) REVERT: B 482 ASN cc_start: 0.6801 (t0) cc_final: 0.6138 (t0) REVERT: B 492 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8348 (mmp80) outliers start: 32 outliers final: 8 residues processed: 242 average time/residue: 1.1078 time to fit residues: 298.0385 Evaluate side-chains 215 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN C 279 HIS C 355 HIS ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS A 355 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 355 HIS B 408 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147509 restraints weight = 15926.486| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 0.91 r_work: 0.3593 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15152 Z= 0.162 Angle : 0.514 5.265 20512 Z= 0.272 Chirality : 0.041 0.127 2276 Planarity : 0.004 0.050 2604 Dihedral : 10.060 112.609 2292 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.75 % Allowed : 14.58 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1920 helix: 1.01 (0.14), residues: 1308 sheet: 0.54 (0.71), residues: 48 loop : 0.17 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 281 HIS 0.005 0.001 HIS C 421 PHE 0.023 0.001 PHE B 141 TYR 0.023 0.002 TYR C 411 ARG 0.011 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1017) hydrogen bonds : angle 4.78457 ( 3015) covalent geometry : bond 0.00363 (15152) covalent geometry : angle 0.51366 (20512) *********************** 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 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.619 Fit side-chains REVERT: D 113 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7775 (tpp) REVERT: D 118 LYS cc_start: 0.8127 (tptp) cc_final: 0.7706 (tttt) REVERT: D 258 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6159 (ttt180) REVERT: D 283 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6970 (mm-30) REVERT: D 287 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6612 (mmt) REVERT: C 113 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7781 (tpp) REVERT: C 118 LYS cc_start: 0.8107 (tptp) cc_final: 0.7695 (tttt) REVERT: C 258 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6166 (ttt180) REVERT: C 283 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7066 (mm-30) REVERT: C 452 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8246 (mt-10) REVERT: A 113 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7710 (tpp) REVERT: A 118 LYS cc_start: 0.8103 (tptp) cc_final: 0.7705 (tttt) REVERT: A 258 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6116 (ttt180) REVERT: A 283 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7145 (pt0) REVERT: A 287 MET cc_start: 0.7173 (mmt) cc_final: 0.6384 (mmt) REVERT: B 118 LYS cc_start: 0.8081 (tptp) cc_final: 0.7689 (tttt) REVERT: B 141 PHE cc_start: 0.8024 (t80) cc_final: 0.7770 (t80) REVERT: B 258 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6167 (ttt180) REVERT: B 283 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7010 (mm-30) REVERT: B 287 MET cc_start: 0.7159 (mmt) cc_final: 0.6350 (mmt) REVERT: B 452 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8093 (mt-10) outliers start: 37 outliers final: 13 residues processed: 233 average time/residue: 1.1504 time to fit residues: 298.2911 Evaluate side-chains 218 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 258 ARG Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 113 MET 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 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 258 ARG Chi-restraints excluded: chain A residue 426 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 46 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 408 GLN 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 = 0.3958 r_free = 0.3958 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149311 restraints weight = 16130.737| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 0.99 r_work: 0.3628 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3018 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= 0.131 Angle : 0.487 4.844 20512 Z= 0.258 Chirality : 0.040 0.121 2276 Planarity : 0.004 0.046 2604 Dihedral : 9.342 99.653 2292 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.90 % Allowed : 15.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1920 helix: 1.24 (0.14), residues: 1304 sheet: 0.43 (0.67), residues: 48 loop : 0.11 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.015 0.001 PHE B 141 TYR 0.021 0.002 TYR D 411 ARG 0.008 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1017) hydrogen bonds : angle 4.63717 ( 3015) covalent geometry : bond 0.00287 (15152) covalent geometry : angle 0.48679 (20512) *********************** 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 251 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.725 Fit side-chains REVERT: D 113 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7744 (tpp) REVERT: D 118 LYS cc_start: 0.8078 (tptp) cc_final: 0.7662 (tttt) REVERT: D 258 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6041 (ttt180) REVERT: D 283 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6893 (mm-30) REVERT: D 369 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7686 (ttt) REVERT: D 482 ASN cc_start: 0.6809 (t0) cc_final: 0.6188 (t0) REVERT: C 113 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7646 (tpp) REVERT: C 118 LYS cc_start: 0.8106 (tptp) cc_final: 0.7682 (tttt) REVERT: C 238 ILE cc_start: 0.7375 (mm) cc_final: 0.7154 (mm) REVERT: C 258 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6081 (ttt180) REVERT: C 287 MET cc_start: 0.7077 (mmt) cc_final: 0.6271 (mmt) REVERT: C 369 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7663 (ttt) REVERT: C 482 ASN cc_start: 0.6804 (t0) cc_final: 0.6163 (t0) REVERT: A 113 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7646 (tpp) REVERT: A 118 LYS cc_start: 0.8068 (tptp) cc_final: 0.7662 (tttt) REVERT: A 258 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6043 (ttt180) REVERT: A 283 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6981 (pt0) REVERT: A 287 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6235 (mmt) REVERT: A 482 ASN cc_start: 0.6803 (t0) cc_final: 0.6158 (t0) REVERT: B 118 LYS cc_start: 0.8097 (tptp) cc_final: 0.7682 (tttt) REVERT: B 232 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7662 (t) REVERT: B 258 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6078 (ttt180) REVERT: B 283 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6825 (mm-30) REVERT: B 287 MET cc_start: 0.7062 (mmt) cc_final: 0.6220 (mmt) REVERT: B 369 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7655 (ttt) REVERT: B 452 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 482 ASN cc_start: 0.6818 (t0) cc_final: 0.6188 (t0) outliers start: 39 outliers final: 15 residues processed: 238 average time/residue: 1.0794 time to fit residues: 287.0759 Evaluate side-chains 221 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 140 ASP 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 369 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 140 ASP 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 369 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 140 ASP 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 369 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 92 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 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 355 HIS C 355 HIS A 355 HIS B 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149083 restraints weight = 16211.993| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.05 r_work: 0.3632 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3124 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= 0.139 Angle : 0.491 5.148 20512 Z= 0.258 Chirality : 0.040 0.135 2276 Planarity : 0.004 0.054 2604 Dihedral : 8.801 87.893 2292 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.60 % Allowed : 16.89 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 1920 helix: 1.29 (0.14), residues: 1312 sheet: 0.35 (0.60), residues: 68 loop : 0.23 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.027 0.001 PHE D 141 TYR 0.021 0.002 TYR C 411 ARG 0.005 0.000 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 1017) hydrogen bonds : angle 4.59601 ( 3015) covalent geometry : bond 0.00307 (15152) covalent geometry : angle 0.49067 (20512) *********************** 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 238 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.612 Fit side-chains REVERT: D 118 LYS cc_start: 0.8072 (tptp) cc_final: 0.7592 (tttt) REVERT: D 232 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7677 (t) REVERT: D 258 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6023 (ttt180) REVERT: D 283 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6838 (mm-30) REVERT: C 118 LYS cc_start: 0.8050 (tptp) cc_final: 0.7614 (tttt) REVERT: C 232 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (t) REVERT: C 258 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6053 (ttt180) REVERT: C 283 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6851 (mm-30) REVERT: C 287 MET cc_start: 0.7063 (mmt) cc_final: 0.6227 (mmt) REVERT: A 118 LYS cc_start: 0.8063 (tptp) cc_final: 0.7577 (tttt) REVERT: A 232 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7663 (t) REVERT: A 258 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5994 (ttt180) REVERT: A 287 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6172 (mmt) REVERT: B 118 LYS cc_start: 0.8028 (tptp) cc_final: 0.7574 (tttt) REVERT: B 141 PHE cc_start: 0.8014 (t80) cc_final: 0.7695 (t80) REVERT: B 232 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7668 (t) REVERT: B 258 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6026 (ttt180) REVERT: B 283 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6829 (mm-30) REVERT: B 287 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6172 (mmt) REVERT: B 452 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8075 (mt-10) outliers start: 35 outliers final: 9 residues processed: 228 average time/residue: 1.0956 time to fit residues: 278.4451 Evaluate side-chains 215 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 426 ASP Chi-restraints excluded: chain C residue 140 ASP 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 134 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148157 restraints weight = 16317.295| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.87 r_work: 0.3590 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.156 Angle : 0.512 5.810 20512 Z= 0.269 Chirality : 0.041 0.129 2276 Planarity : 0.004 0.050 2604 Dihedral : 8.568 78.009 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.46 % Allowed : 17.04 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1920 helix: 1.30 (0.14), residues: 1312 sheet: 0.48 (0.61), residues: 68 loop : 0.18 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 281 HIS 0.005 0.001 HIS C 421 PHE 0.015 0.001 PHE C 236 TYR 0.022 0.002 TYR A 411 ARG 0.005 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1017) hydrogen bonds : angle 4.61443 ( 3015) covalent geometry : bond 0.00350 (15152) covalent geometry : angle 0.51153 (20512) *********************** 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 232 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.656 Fit side-chains REVERT: D 113 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7743 (tpp) REVERT: D 118 LYS cc_start: 0.8109 (tptp) cc_final: 0.7634 (tttt) REVERT: D 232 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7716 (t) REVERT: D 258 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6099 (ttt180) REVERT: D 283 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7010 (mm-30) REVERT: D 482 ASN cc_start: 0.6676 (t0) cc_final: 0.6140 (t0) REVERT: C 113 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7704 (tpp) REVERT: C 118 LYS cc_start: 0.8095 (tptp) cc_final: 0.7612 (tttt) REVERT: C 232 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7704 (t) REVERT: C 258 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6137 (ttt180) REVERT: C 283 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7011 (mm-30) REVERT: C 287 MET cc_start: 0.7169 (mmt) cc_final: 0.6375 (mmt) REVERT: C 482 ASN cc_start: 0.6732 (t0) cc_final: 0.6204 (t0) REVERT: A 113 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7670 (tpp) REVERT: A 118 LYS cc_start: 0.8089 (tptp) cc_final: 0.7632 (tttt) REVERT: A 232 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7750 (t) REVERT: A 258 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6103 (ttt180) REVERT: A 287 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6341 (mmt) REVERT: A 482 ASN cc_start: 0.6734 (t0) cc_final: 0.6254 (t0) REVERT: B 118 LYS cc_start: 0.8069 (tptp) cc_final: 0.7584 (tttt) REVERT: B 258 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6146 (ttt180) REVERT: B 283 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7008 (mm-30) REVERT: B 287 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6313 (mmt) REVERT: B 452 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 482 ASN cc_start: 0.6673 (t0) cc_final: 0.6134 (t0) outliers start: 33 outliers final: 16 residues processed: 219 average time/residue: 1.1226 time to fit residues: 273.3279 Evaluate side-chains 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 ASP 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 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 140 ASP 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 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 140 ASP 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 321 LEU 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 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 60 optimal weight: 0.7980 chunk 157 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS C 355 HIS A 355 HIS B 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149353 restraints weight = 16223.460| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.01 r_work: 0.3575 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3275 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= 0.130 Angle : 0.492 5.547 20512 Z= 0.258 Chirality : 0.040 0.126 2276 Planarity : 0.004 0.050 2604 Dihedral : 8.248 69.141 2292 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.83 % Allowed : 16.67 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 1920 helix: 1.39 (0.14), residues: 1312 sheet: 0.55 (0.59), residues: 68 loop : 0.24 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 PHE 0.025 0.001 PHE B 141 TYR 0.020 0.002 TYR D 411 ARG 0.005 0.000 ARG C 554 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1017) hydrogen bonds : angle 4.54321 ( 3015) covalent geometry : bond 0.00286 (15152) covalent geometry : angle 0.49197 (20512) *********************** 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 242 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.568 Fit side-chains REVERT: D 113 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7545 (tpp) REVERT: D 118 LYS cc_start: 0.7949 (tptp) cc_final: 0.7493 (tttt) REVERT: D 238 ILE cc_start: 0.7440 (mm) cc_final: 0.7196 (mm) REVERT: D 258 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5971 (ttt180) REVERT: D 287 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6214 (mmm) REVERT: C 118 LYS cc_start: 0.7940 (tptp) cc_final: 0.7555 (tttt) REVERT: C 238 ILE cc_start: 0.7354 (mp) cc_final: 0.7116 (mm) REVERT: C 258 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6011 (ttt180) REVERT: A 113 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7628 (tpp) REVERT: A 118 LYS cc_start: 0.7940 (tptp) cc_final: 0.7494 (tttt) REVERT: A 238 ILE cc_start: 0.7360 (mp) cc_final: 0.7040 (mm) REVERT: A 258 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5969 (ttt180) REVERT: B 118 LYS cc_start: 0.7914 (tptp) cc_final: 0.7554 (tttt) REVERT: B 258 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6019 (ttt180) REVERT: B 287 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6088 (mmt) REVERT: B 452 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8031 (mt-10) outliers start: 38 outliers final: 11 residues processed: 226 average time/residue: 1.0993 time to fit residues: 278.1356 Evaluate side-chains 214 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 ASP 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 450 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 140 ASP 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 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 167 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 chunk 166 optimal weight: 0.0010 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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 156 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 156 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 = 0.3984 r_free = 0.3984 target = 0.166566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152740 restraints weight = 16161.785| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 0.87 r_work: 0.3624 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15152 Z= 0.118 Angle : 0.496 6.893 20512 Z= 0.260 Chirality : 0.039 0.129 2276 Planarity : 0.004 0.050 2604 Dihedral : 7.906 58.593 2292 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.16 % Allowed : 17.34 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 1920 helix: 1.46 (0.14), residues: 1316 sheet: 0.54 (0.61), residues: 48 loop : 0.27 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.018 0.001 PHE C 236 TYR 0.018 0.001 TYR B 411 ARG 0.004 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1017) hydrogen bonds : angle 4.43775 ( 3015) covalent geometry : bond 0.00250 (15152) covalent geometry : angle 0.49589 (20512) *********************** 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 234 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.675 Fit side-chains REVERT: D 113 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7743 (tpp) REVERT: D 118 LYS cc_start: 0.8076 (tptp) cc_final: 0.7661 (tttt) REVERT: D 285 PHE cc_start: 0.8023 (m-10) cc_final: 0.7809 (m-10) REVERT: D 287 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6417 (mmm) REVERT: D 369 MET cc_start: 0.7745 (ttm) cc_final: 0.7491 (ttt) REVERT: C 113 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7745 (tpp) REVERT: C 118 LYS cc_start: 0.8080 (tptp) cc_final: 0.7664 (tttt) REVERT: C 238 ILE cc_start: 0.7310 (mp) cc_final: 0.7044 (mm) REVERT: A 113 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7770 (tpp) REVERT: A 118 LYS cc_start: 0.8056 (tptp) cc_final: 0.7655 (tttt) REVERT: A 238 ILE cc_start: 0.7474 (mp) cc_final: 0.7115 (mm) REVERT: B 118 LYS cc_start: 0.8068 (tptp) cc_final: 0.7617 (tttt) REVERT: B 238 ILE cc_start: 0.7429 (mp) cc_final: 0.7120 (mm) REVERT: B 369 MET cc_start: 0.7751 (ttm) cc_final: 0.7503 (ttt) REVERT: B 452 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8120 (mt-10) outliers start: 29 outliers final: 8 residues processed: 218 average time/residue: 1.1105 time to fit residues: 270.0791 Evaluate side-chains 213 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 135 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149057 restraints weight = 16333.210| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 0.80 r_work: 0.3590 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15152 Z= 0.173 Angle : 0.551 8.205 20512 Z= 0.285 Chirality : 0.041 0.127 2276 Planarity : 0.004 0.051 2604 Dihedral : 8.090 59.783 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.26 % Allowed : 18.53 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1920 helix: 1.32 (0.14), residues: 1316 sheet: 0.29 (0.61), residues: 48 loop : 0.23 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 281 HIS 0.006 0.001 HIS D 421 PHE 0.023 0.002 PHE C 236 TYR 0.022 0.002 TYR B 411 ARG 0.005 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1017) hydrogen bonds : angle 4.60593 ( 3015) covalent geometry : bond 0.00396 (15152) covalent geometry : angle 0.55054 (20512) ********************** 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: 17 poor density : 193 time to evaluate : 1.712 Fit side-chains REVERT: D 113 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7722 (tpp) REVERT: D 118 LYS cc_start: 0.8095 (tptp) cc_final: 0.7607 (tttt) REVERT: D 238 ILE cc_start: 0.7446 (mp) cc_final: 0.7127 (mm) REVERT: D 287 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6629 (mmm) REVERT: C 113 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7717 (tpp) REVERT: C 118 LYS cc_start: 0.8078 (tptp) cc_final: 0.7594 (tttt) REVERT: C 238 ILE cc_start: 0.7411 (mp) cc_final: 0.7128 (mm) REVERT: A 113 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: A 118 LYS cc_start: 0.8075 (tptp) cc_final: 0.7587 (tttt) REVERT: A 238 ILE cc_start: 0.7484 (mp) cc_final: 0.7183 (mm) REVERT: B 118 LYS cc_start: 0.8068 (tptp) cc_final: 0.7597 (tttt) REVERT: B 238 ILE cc_start: 0.7430 (mp) cc_final: 0.7123 (mm) REVERT: B 452 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8278 (mt-10) outliers start: 17 outliers final: 12 residues processed: 204 average time/residue: 1.1876 time to fit residues: 269.2714 Evaluate side-chains 208 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 287 MET 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 113 MET Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 482 ASN C 355 HIS C 482 ASN A 355 HIS A 482 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151843 restraints weight = 16296.650| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 0.75 r_work: 0.3626 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3465 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= 0.125 Angle : 0.514 9.104 20512 Z= 0.266 Chirality : 0.040 0.124 2276 Planarity : 0.004 0.049 2604 Dihedral : 7.585 59.814 2292 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.82 % Allowed : 18.97 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1920 helix: 1.41 (0.14), residues: 1316 sheet: 0.54 (0.59), residues: 48 loop : 0.29 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 281 HIS 0.004 0.001 HIS D 421 PHE 0.015 0.001 PHE C 141 TYR 0.019 0.001 TYR C 411 ARG 0.005 0.001 ARG C 554 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1017) hydrogen bonds : angle 4.48418 ( 3015) covalent geometry : bond 0.00274 (15152) covalent geometry : angle 0.51396 (20512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9470.32 seconds wall clock time: 164 minutes 28.47 seconds (9868.47 seconds total)