Starting phenix.real_space_refine on Fri Jun 13 06:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc8_42117/06_2025/8uc8_42117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc8_42117/06_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_42117/06_2025/8uc8_42117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc8_42117/06_2025/8uc8_42117.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc8_42117/06_2025/8uc8_42117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc8_42117/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.00, per 1000 atoms: 0.54 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: 3.26 Conformation dependent library (CDL) restraints added in 1.8 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: 1.44 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: 4.80 Time building geometry restraints manager: 3.93 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.720 Find NCS groups from input model: 1.060 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: 0.010 Load rotamer database and sin/cos tables:15.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.200 ------------------------------------------------------------------------------- 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 : 1.582 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: 1.1557 time to fit residues: 448.9162 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 : 1.490 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154842 restraints weight = 15811.165| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.60 r_work: 0.3660 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 1.505 Fit side-chains revert: symmetry clash REVERT: D 118 LYS cc_start: 0.8102 (tptp) cc_final: 0.7854 (tttt) REVERT: D 184 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7741 (p) REVERT: D 258 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6463 (ttt180) REVERT: D 287 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: D 401 ASP cc_start: 0.7841 (p0) cc_final: 0.7625 (p0) REVERT: D 460 GLU cc_start: 0.8536 (tt0) cc_final: 0.8295 (mt-10) REVERT: C 118 LYS cc_start: 0.8098 (tptp) cc_final: 0.7867 (tttt) REVERT: C 184 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7742 (p) REVERT: C 258 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6436 (ttt180) REVERT: C 287 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7524 (mmm) REVERT: C 401 ASP cc_start: 0.7846 (p0) cc_final: 0.7644 (p0) REVERT: A 118 LYS cc_start: 0.8122 (tptp) cc_final: 0.7869 (tttt) REVERT: A 184 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 258 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6489 (ttt180) REVERT: A 460 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: B 118 LYS cc_start: 0.8096 (tptp) cc_final: 0.7877 (tttt) REVERT: B 184 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 238 ILE cc_start: 0.7575 (mp) cc_final: 0.7296 (mm) REVERT: B 258 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6492 (ttt180) outliers start: 37 outliers final: 8 residues processed: 278 average time/residue: 1.2491 time to fit residues: 382.6180 Evaluate side-chains 216 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 4.9990 chunk 183 optimal weight: 0.0020 chunk 150 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.165058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150843 restraints weight = 15996.660| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 0.88 r_work: 0.3630 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.136 Angle : 0.504 5.201 20512 Z= 0.271 Chirality : 0.041 0.128 2276 Planarity : 0.004 0.049 2604 Dihedral : 10.917 132.905 2292 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.01 % Allowed : 13.76 % 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: 1.01 (0.19), residues: 1920 helix: 0.93 (0.14), residues: 1304 sheet: 1.03 (0.71), residues: 48 loop : 0.30 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 281 HIS 0.005 0.001 HIS C 421 PHE 0.014 0.001 PHE D 236 TYR 0.021 0.002 TYR B 411 ARG 0.005 0.001 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1017) hydrogen bonds : angle 4.85444 ( 3015) covalent geometry : bond 0.00290 (15152) covalent geometry : angle 0.50361 (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 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 1.591 Fit side-chains REVERT: D 118 LYS cc_start: 0.8115 (tptp) cc_final: 0.7796 (tttt) REVERT: D 287 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6980 (mmm) REVERT: D 452 GLU cc_start: 0.8212 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 482 ASN cc_start: 0.6778 (t0) cc_final: 0.6051 (t0) REVERT: D 492 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8315 (mmp80) REVERT: C 118 LYS cc_start: 0.8066 (tptp) cc_final: 0.7773 (tttt) REVERT: C 283 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6841 (mm-30) REVERT: C 287 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7002 (mmm) REVERT: C 482 ASN cc_start: 0.6704 (t0) cc_final: 0.6000 (t0) REVERT: C 492 ARG cc_start: 0.8613 (mmp80) cc_final: 0.8291 (mmp80) REVERT: A 118 LYS cc_start: 0.8102 (tptp) cc_final: 0.7800 (tttt) REVERT: A 482 ASN cc_start: 0.6829 (t0) cc_final: 0.6154 (t0) REVERT: A 492 ARG cc_start: 0.8664 (mmp80) cc_final: 0.8388 (mmp80) REVERT: B 118 LYS cc_start: 0.8053 (tptp) cc_final: 0.7769 (tttt) REVERT: B 192 MET cc_start: 0.7475 (mpt) cc_final: 0.7271 (mpt) REVERT: B 283 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6831 (mm-30) REVERT: B 452 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 482 ASN cc_start: 0.6829 (t0) cc_final: 0.6145 (t0) REVERT: B 492 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8336 (mmp80) outliers start: 27 outliers final: 8 residues processed: 238 average time/residue: 1.4555 time to fit residues: 383.3586 Evaluate side-chains 212 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 426 ASP 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: 0.9980 chunk 106 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 C 279 HIS C 355 HIS A 279 HIS A 355 HIS B 279 HIS B 355 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144729 restraints weight = 16056.740| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 0.90 r_work: 0.3571 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15152 Z= 0.207 Angle : 0.551 6.276 20512 Z= 0.291 Chirality : 0.042 0.130 2276 Planarity : 0.004 0.051 2604 Dihedral : 10.269 113.903 2292 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.35 % Allowed : 14.51 % Favored : 82.14 % 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: 0.84 (0.19), residues: 1920 helix: 0.89 (0.14), residues: 1304 sheet: 0.53 (0.71), residues: 48 loop : -0.00 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 281 HIS 0.006 0.001 HIS D 421 PHE 0.020 0.002 PHE B 141 TYR 0.025 0.002 TYR C 411 ARG 0.007 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1017) hydrogen bonds : angle 4.91227 ( 3015) covalent geometry : bond 0.00472 (15152) covalent geometry : angle 0.55137 (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 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.754 Fit side-chains REVERT: D 113 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7806 (tpp) REVERT: D 118 LYS cc_start: 0.8075 (tptp) cc_final: 0.7710 (tttt) REVERT: D 258 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6212 (ttt180) REVERT: D 283 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7095 (mm-30) REVERT: D 287 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6651 (mmt) REVERT: D 369 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7896 (ttm) REVERT: C 113 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7833 (tpp) REVERT: C 118 LYS cc_start: 0.8061 (tptp) cc_final: 0.7675 (tttt) REVERT: C 258 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6199 (ttt180) REVERT: C 283 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7132 (mm-30) REVERT: C 287 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6664 (mmt) REVERT: C 369 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: A 113 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: A 118 LYS cc_start: 0.8054 (tptp) cc_final: 0.7687 (tttt) REVERT: A 258 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6163 (ttt180) REVERT: A 283 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7202 (pt0) REVERT: A 287 MET cc_start: 0.7201 (mmt) cc_final: 0.6417 (mmt) REVERT: A 452 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 118 LYS cc_start: 0.8055 (tptp) cc_final: 0.7684 (tttt) REVERT: B 238 ILE cc_start: 0.7520 (mm) cc_final: 0.7272 (mm) REVERT: B 258 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6189 (ttt180) REVERT: B 283 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7097 (mm-30) REVERT: B 287 MET cc_start: 0.7190 (mmt) cc_final: 0.6395 (mmt) REVERT: B 369 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7856 (ttm) REVERT: B 452 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8099 (mt-10) outliers start: 45 outliers final: 13 residues processed: 236 average time/residue: 1.2243 time to fit residues: 320.7214 Evaluate side-chains 221 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 369 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 287 MET 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 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 369 MET 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: 0.5980 chunk 132 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 146 optimal weight: 0.0970 chunk 182 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 98 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS D 408 GLN 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 408 GLN B 482 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149744 restraints weight = 16126.178| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 0.95 r_work: 0.3567 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.121 Angle : 0.485 4.919 20512 Z= 0.257 Chirality : 0.040 0.130 2276 Planarity : 0.004 0.046 2604 Dihedral : 9.482 99.917 2292 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.23 % Allowed : 16.00 % Favored : 81.77 % 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: 1.23 (0.19), residues: 1920 helix: 1.20 (0.14), residues: 1304 sheet: 0.50 (0.68), residues: 48 loop : 0.13 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.013 0.001 PHE C 236 TYR 0.021 0.001 TYR C 411 ARG 0.007 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 1017) hydrogen bonds : angle 4.66054 ( 3015) covalent geometry : bond 0.00259 (15152) covalent geometry : angle 0.48524 (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 239 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.489 Fit side-chains REVERT: D 113 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7635 (tpp) REVERT: D 118 LYS cc_start: 0.7949 (tptp) cc_final: 0.7564 (tttt) REVERT: D 238 ILE cc_start: 0.7449 (mm) cc_final: 0.7238 (mm) REVERT: D 258 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6045 (ttt180) REVERT: D 283 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6798 (mm-30) REVERT: D 482 ASN cc_start: 0.6748 (t0) cc_final: 0.6104 (t0) REVERT: C 113 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7576 (tpp) REVERT: C 118 LYS cc_start: 0.7945 (tptp) cc_final: 0.7579 (tttt) REVERT: C 238 ILE cc_start: 0.7363 (mm) cc_final: 0.7157 (mm) REVERT: C 258 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6060 (ttt180) REVERT: A 113 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7577 (tpp) REVERT: A 118 LYS cc_start: 0.7953 (tptp) cc_final: 0.7575 (tttt) REVERT: A 258 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6032 (ttt180) REVERT: A 287 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6131 (mmt) REVERT: A 482 ASN cc_start: 0.6686 (t0) cc_final: 0.6108 (t0) REVERT: B 118 LYS cc_start: 0.7935 (tptp) cc_final: 0.7599 (tttt) REVERT: B 141 PHE cc_start: 0.8016 (t80) cc_final: 0.7733 (t80) REVERT: B 192 MET cc_start: 0.7179 (mpt) cc_final: 0.6964 (mpt) REVERT: B 258 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6031 (ttt180) REVERT: B 283 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6828 (mm-30) REVERT: B 287 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6133 (mmt) REVERT: B 452 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 482 ASN cc_start: 0.6798 (t0) cc_final: 0.6189 (t0) outliers start: 30 outliers final: 12 residues processed: 226 average time/residue: 1.2998 time to fit residues: 325.7376 Evaluate side-chains 212 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 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 C 355 HIS C 482 ASN A 355 HIS B 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150332 restraints weight = 16215.476| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 0.88 r_work: 0.3652 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3123 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= 0.134 Angle : 0.501 5.655 20512 Z= 0.261 Chirality : 0.040 0.134 2276 Planarity : 0.004 0.053 2604 Dihedral : 8.990 90.406 2292 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.68 % Allowed : 16.89 % Favored : 80.43 % 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: 1.32 (0.19), residues: 1920 helix: 1.26 (0.14), residues: 1312 sheet: 0.39 (0.66), residues: 48 loop : 0.19 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 281 HIS 0.004 0.001 HIS C 421 PHE 0.025 0.001 PHE D 141 TYR 0.021 0.002 TYR C 411 ARG 0.005 0.001 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1017) hydrogen bonds : angle 4.59492 ( 3015) covalent geometry : bond 0.00292 (15152) covalent geometry : angle 0.50106 (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 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.803 Fit side-chains REVERT: D 113 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7580 (tpp) REVERT: D 118 LYS cc_start: 0.8057 (tptp) cc_final: 0.7565 (tttt) REVERT: D 232 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7678 (t) REVERT: D 258 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6017 (ttt180) REVERT: D 283 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6835 (mm-30) REVERT: D 287 MET cc_start: 0.7038 (mmt) cc_final: 0.6215 (mmt) REVERT: C 113 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7666 (tpp) REVERT: C 118 LYS cc_start: 0.8032 (tptp) cc_final: 0.7574 (tttt) REVERT: C 232 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 258 ARG cc_start: 0.6497 (OUTLIER) cc_final: 0.6023 (ttt180) REVERT: C 283 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6842 (mm-30) REVERT: C 287 MET cc_start: 0.7073 (mmt) cc_final: 0.6256 (mmt) REVERT: C 482 ASN cc_start: 0.6632 (t0) cc_final: 0.6143 (t0) REVERT: A 118 LYS cc_start: 0.8039 (tptp) cc_final: 0.7576 (tttt) REVERT: A 232 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7675 (t) REVERT: A 258 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6003 (ttt180) REVERT: A 287 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6171 (mmt) REVERT: B 118 LYS cc_start: 0.8027 (tptp) cc_final: 0.7576 (tttt) REVERT: B 141 PHE cc_start: 0.7985 (t80) cc_final: 0.7723 (t80) REVERT: B 232 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7628 (t) REVERT: B 258 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.6020 (ttt180) REVERT: B 283 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6816 (mm-30) REVERT: B 287 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6149 (mmt) REVERT: B 452 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8029 (mt-10) outliers start: 36 outliers final: 10 residues processed: 227 average time/residue: 1.2728 time to fit residues: 322.0445 Evaluate side-chains 219 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 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 A residue 460 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 426 ASP 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: 0.6980 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 0.0070 chunk 81 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 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 = 0.3972 r_free = 0.3972 target = 0.165521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150794 restraints weight = 16295.056| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.97 r_work: 0.3648 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3250 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= 0.124 Angle : 0.491 5.250 20512 Z= 0.257 Chirality : 0.040 0.125 2276 Planarity : 0.004 0.050 2604 Dihedral : 8.387 76.875 2292 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.05 % Allowed : 16.59 % Favored : 80.36 % 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: 1.50 (0.19), residues: 1920 helix: 1.39 (0.14), residues: 1316 sheet: 0.56 (0.60), residues: 68 loop : 0.29 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 281 HIS 0.004 0.001 HIS C 421 PHE 0.021 0.001 PHE D 141 TYR 0.020 0.001 TYR D 411 ARG 0.005 0.000 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1017) hydrogen bonds : angle 4.50566 ( 3015) covalent geometry : bond 0.00270 (15152) covalent geometry : angle 0.49069 (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 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 1.723 Fit side-chains REVERT: D 118 LYS cc_start: 0.8078 (tptp) cc_final: 0.7608 (tttt) REVERT: D 258 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.5999 (ttt180) REVERT: D 369 MET cc_start: 0.7776 (ttm) cc_final: 0.7556 (ttt) REVERT: D 482 ASN cc_start: 0.6753 (t0) cc_final: 0.6162 (t0) REVERT: C 118 LYS cc_start: 0.8064 (tptp) cc_final: 0.7589 (tttt) REVERT: C 258 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6061 (ttt180) REVERT: C 369 MET cc_start: 0.7797 (ttm) cc_final: 0.7574 (ttt) REVERT: A 113 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7718 (tpp) REVERT: A 118 LYS cc_start: 0.8051 (tptp) cc_final: 0.7590 (tttt) REVERT: A 258 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6046 (ttt180) REVERT: A 287 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6215 (mmt) REVERT: A 482 ASN cc_start: 0.6744 (t0) cc_final: 0.6133 (t0) REVERT: B 118 LYS cc_start: 0.8051 (tptp) cc_final: 0.7588 (tttt) REVERT: B 141 PHE cc_start: 0.7954 (t80) cc_final: 0.7644 (t80) REVERT: B 258 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6070 (ttt180) REVERT: B 287 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6137 (mmt) REVERT: B 369 MET cc_start: 0.7800 (ttm) cc_final: 0.7581 (ttt) REVERT: B 452 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 482 ASN cc_start: 0.6761 (t0) cc_final: 0.6156 (t0) outliers start: 41 outliers final: 13 residues processed: 232 average time/residue: 1.1546 time to fit residues: 297.7661 Evaluate side-chains 220 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE 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 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 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: 3.9990 chunk 138 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 C 482 ASN A 355 HIS B 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149331 restraints weight = 16291.817| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.95 r_work: 0.3631 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3273 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= 0.148 Angle : 0.522 5.882 20512 Z= 0.271 Chirality : 0.040 0.131 2276 Planarity : 0.004 0.058 2604 Dihedral : 8.300 69.329 2292 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.46 % Allowed : 17.26 % Favored : 80.28 % 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: 1.44 (0.19), residues: 1920 helix: 1.37 (0.14), residues: 1312 sheet: 0.48 (0.60), residues: 68 loop : 0.20 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 281 HIS 0.006 0.001 HIS D 421 PHE 0.018 0.001 PHE A 236 TYR 0.021 0.002 TYR C 411 ARG 0.005 0.001 ARG C 554 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 1017) hydrogen bonds : angle 4.54580 ( 3015) covalent geometry : bond 0.00333 (15152) covalent geometry : angle 0.52159 (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 234 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.727 Fit side-chains REVERT: D 118 LYS cc_start: 0.8020 (tptp) cc_final: 0.7604 (tttt) REVERT: D 238 ILE cc_start: 0.7343 (mp) cc_final: 0.7087 (mm) REVERT: D 258 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6030 (ttt180) REVERT: C 113 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7712 (tpp) REVERT: C 118 LYS cc_start: 0.8026 (tptp) cc_final: 0.7604 (tttt) REVERT: C 238 ILE cc_start: 0.7279 (mp) cc_final: 0.7031 (mm) REVERT: C 258 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6050 (ttt180) REVERT: C 482 ASN cc_start: 0.6696 (t0) cc_final: 0.6197 (t0) REVERT: A 113 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7700 (tpp) REVERT: A 118 LYS cc_start: 0.8006 (tptp) cc_final: 0.7592 (tttt) REVERT: A 258 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6052 (ttt180) REVERT: B 118 LYS cc_start: 0.8012 (tptp) cc_final: 0.7604 (tttt) REVERT: B 238 ILE cc_start: 0.7436 (mm) cc_final: 0.7202 (mm) REVERT: B 258 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6062 (ttt180) REVERT: B 452 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8143 (mt-10) outliers start: 33 outliers final: 12 residues processed: 218 average time/residue: 1.2374 time to fit residues: 301.6611 Evaluate side-chains 216 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 135 ILE 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 135 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 321 LEU 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: 1.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 167 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.0000 chunk 166 optimal weight: 0.0070 overall best weight: 0.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 ASN D 355 HIS D 482 ASN C 156 ASN C 355 HIS A 156 ASN A 355 HIS A 482 ASN B 156 ASN B 355 HIS B 482 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.168336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155466 restraints weight = 16131.921| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 0.69 r_work: 0.3663 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15152 Z= 0.109 Angle : 0.487 6.608 20512 Z= 0.254 Chirality : 0.039 0.124 2276 Planarity : 0.004 0.059 2604 Dihedral : 7.892 57.484 2292 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 18.08 % Favored : 80.58 % 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: 1.65 (0.20), residues: 1920 helix: 1.51 (0.14), residues: 1316 sheet: 0.55 (0.59), residues: 48 loop : 0.32 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 281 HIS 0.004 0.001 HIS C 421 PHE 0.027 0.001 PHE B 141 TYR 0.017 0.001 TYR A 411 ARG 0.005 0.001 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1017) hydrogen bonds : angle 4.39469 ( 3015) covalent geometry : bond 0.00230 (15152) covalent geometry : angle 0.48705 (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 223 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 3.569 Fit side-chains REVERT: D 118 LYS cc_start: 0.8160 (tptp) cc_final: 0.7707 (tttt) REVERT: D 238 ILE cc_start: 0.7313 (mp) cc_final: 0.7081 (mm) REVERT: D 285 PHE cc_start: 0.8064 (m-10) cc_final: 0.7837 (m-10) REVERT: D 369 MET cc_start: 0.7738 (ttm) cc_final: 0.7500 (ttt) REVERT: C 118 LYS cc_start: 0.8137 (tptp) cc_final: 0.7678 (tttt) REVERT: C 238 ILE cc_start: 0.7353 (mp) cc_final: 0.7115 (mm) REVERT: C 285 PHE cc_start: 0.8078 (m-10) cc_final: 0.7871 (m-10) REVERT: C 369 MET cc_start: 0.7745 (ttm) cc_final: 0.7508 (ttt) REVERT: A 113 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7757 (tpp) REVERT: A 118 LYS cc_start: 0.8156 (tptp) cc_final: 0.7703 (tttt) REVERT: A 238 ILE cc_start: 0.7438 (mp) cc_final: 0.7125 (mm) REVERT: B 118 LYS cc_start: 0.8127 (tptp) cc_final: 0.7681 (tttt) REVERT: B 238 ILE cc_start: 0.7524 (mm) cc_final: 0.7271 (mm) REVERT: B 369 MET cc_start: 0.7729 (ttm) cc_final: 0.7488 (ttt) REVERT: B 452 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 18 outliers final: 10 residues processed: 214 average time/residue: 1.3017 time to fit residues: 312.0481 Evaluate side-chains 208 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 426 ASP 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 151 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145098 restraints weight = 16486.900| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.64 r_work: 0.3558 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15152 Z= 0.280 Angle : 0.652 8.630 20512 Z= 0.334 Chirality : 0.045 0.123 2276 Planarity : 0.005 0.059 2604 Dihedral : 8.915 64.137 2292 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.41 % Allowed : 18.45 % Favored : 80.13 % 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: 0.94 (0.19), residues: 1920 helix: 1.04 (0.14), residues: 1304 sheet: 0.27 (0.59), residues: 68 loop : -0.13 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 281 HIS 0.006 0.002 HIS D 421 PHE 0.027 0.002 PHE D 236 TYR 0.026 0.003 TYR A 411 ARG 0.007 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1017) hydrogen bonds : angle 4.92650 ( 3015) covalent geometry : bond 0.00644 (15152) covalent geometry : angle 0.65226 (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 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 2.401 Fit side-chains REVERT: D 118 LYS cc_start: 0.8032 (tptp) cc_final: 0.7577 (tttt) REVERT: D 238 ILE cc_start: 0.7475 (mp) cc_final: 0.7203 (mm) REVERT: C 118 LYS cc_start: 0.8026 (tptp) cc_final: 0.7562 (tttt) REVERT: C 238 ILE cc_start: 0.7602 (mp) cc_final: 0.7321 (mm) REVERT: A 113 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7723 (tpp) REVERT: A 118 LYS cc_start: 0.8032 (tptp) cc_final: 0.7577 (tttt) REVERT: A 238 ILE cc_start: 0.7500 (mp) cc_final: 0.7174 (mm) REVERT: B 118 LYS cc_start: 0.8037 (tptp) cc_final: 0.7583 (tttt) REVERT: B 452 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8277 (mt-10) outliers start: 19 outliers final: 9 residues processed: 194 average time/residue: 1.2878 time to fit residues: 276.6230 Evaluate side-chains 193 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 450 LEU 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: 2.9990 chunk 88 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152306 restraints weight = 16256.428| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.62 r_work: 0.3621 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3466 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= 0.134 Angle : 0.534 9.461 20512 Z= 0.275 Chirality : 0.040 0.122 2276 Planarity : 0.004 0.056 2604 Dihedral : 8.076 59.948 2292 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.19 % Allowed : 18.68 % Favored : 80.13 % 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: 1.33 (0.19), residues: 1920 helix: 1.30 (0.14), residues: 1312 sheet: 0.49 (0.61), residues: 48 loop : 0.09 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 281 HIS 0.005 0.001 HIS D 421 PHE 0.025 0.001 PHE A 141 TYR 0.021 0.002 TYR D 411 ARG 0.005 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1017) hydrogen bonds : angle 4.61446 ( 3015) covalent geometry : bond 0.00297 (15152) covalent geometry : angle 0.53415 (20512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10536.03 seconds wall clock time: 187 minutes 42.70 seconds (11262.70 seconds total)