Starting phenix.real_space_refine on Thu Jul 31 12:03:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2025/8wx0_37896.cif" } resolution = 3.7 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= 0.002 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 49 5.16 5 C 8536 2.51 5 N 2338 2.21 5 O 2738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4478 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 29, 'TRANS': 567} Chain: "B" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 29, 'TRANS': 562} Chain: "C" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4452 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 29, 'TRANS': 563} Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.13, per 1000 atoms: 0.67 Number of scatterers: 13672 At special positions: 0 Unit cell: (110.88, 103.84, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 11 15.00 O 2738 8.00 N 2338 7.00 C 8536 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: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 36.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 115 Proline residue: A 110 - end of helix Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.873A pdb=" N GLN A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.855A pdb=" N GLU A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 344 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.828A pdb=" N THR A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.725A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 584 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 98 through 112 removed outlier: 3.974A pdb=" N CYS B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 138 through 154 removed outlier: 3.844A pdb=" N GLY B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.693A pdb=" N ARG B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.065A pdb=" N SER B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.556A pdb=" N TYR B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.638A pdb=" N LEU B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.924A pdb=" N ILE B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 343 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.507A pdb=" N THR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 558 through 584 removed outlier: 4.146A pdb=" N ALA B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.658A pdb=" N GLY C 23 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 97 through 112 Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 138 through 153 Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.675A pdb=" N GLU C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.523A pdb=" N SER C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 297 through 314 removed outlier: 3.836A pdb=" N ARG C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 304 " --> pdb=" O GLN C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 342 Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.690A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'C' and resid 558 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.095A pdb=" N PHE A 187 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP A 188 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 207 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N MET A 203 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 541 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 535 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 536 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 521 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 362 removed outlier: 6.777A pdb=" N LEU A 382 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA A 462 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 384 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER A 460 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR A 386 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN A 458 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP A 388 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE A 456 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 18 Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.781A pdb=" N ASP B 188 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 207 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N MET B 203 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 551 " --> pdb=" O ASP B 535 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 535 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.200A pdb=" N GLN B 380 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS B 410 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA B 462 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN B 412 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY B 464 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 17 removed outlier: 6.554A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 72 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL C 127 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 74 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE C 129 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU C 76 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER C 131 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 175 removed outlier: 4.197A pdb=" N PHE C 187 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP C 188 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA C 207 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 546 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.338A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 388 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS C 410 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA C 462 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN C 412 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY C 464 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 499 through 506 removed outlier: 3.677A pdb=" N VAL C 513 " --> pdb=" O VAL C 506 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1881 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: 4.64 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4641 1.34 - 1.46: 2024 1.46 - 1.58: 7135 1.58 - 1.70: 22 1.70 - 1.82: 89 Bond restraints: 13911 Sorted by residual: bond pdb=" N PHE B 11 " pdb=" CA PHE B 11 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N VAL B 10 " pdb=" CA VAL B 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.37e-02 5.33e+03 6.31e+00 bond pdb=" N GLY C 498 " pdb=" CA GLY C 498 " ideal model delta sigma weight residual 1.449 1.475 -0.026 1.08e-02 8.57e+03 5.78e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.46e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.30e-02 5.92e+03 4.22e+00 ... (remaining 13906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 18435 1.54 - 3.09: 408 3.09 - 4.63: 75 4.63 - 6.17: 23 6.17 - 7.71: 4 Bond angle restraints: 18945 Sorted by residual: angle pdb=" CA GLY C 498 " pdb=" C GLY C 498 " pdb=" O GLY C 498 " ideal model delta sigma weight residual 122.39 118.18 4.21 1.25e+00 6.40e-01 1.14e+01 angle pdb=" CA GLU C 77 " pdb=" C GLU C 77 " pdb=" O GLU C 77 " ideal model delta sigma weight residual 122.41 118.44 3.97 1.21e+00 6.83e-01 1.07e+01 angle pdb=" N THR B 316 " pdb=" CA THR B 316 " pdb=" C THR B 316 " ideal model delta sigma weight residual 114.56 110.91 3.65 1.27e+00 6.20e-01 8.25e+00 angle pdb=" C VAL C 510 " pdb=" N ASP C 511 " pdb=" CA ASP C 511 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.05e+00 angle pdb=" CA ALA C 496 " pdb=" C ALA C 496 " pdb=" O ALA C 496 " ideal model delta sigma weight residual 121.39 118.27 3.12 1.12e+00 7.97e-01 7.77e+00 ... (remaining 18940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 8061 34.83 - 69.67: 370 69.67 - 104.50: 26 104.50 - 139.34: 0 139.34 - 174.17: 2 Dihedral angle restraints: 8459 sinusoidal: 3401 harmonic: 5058 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 -11.10 -148.90 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U E 6 " pdb=" C1' U E 6 " pdb=" N1 U E 6 " pdb=" C2 U E 6 " ideal model delta sinusoidal sigma weight residual 232.00 57.83 174.17 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C3' U D 1 " pdb=" C4' U D 1 " pdb=" O4' U D 1 " pdb=" C1' U D 1 " ideal model delta sinusoidal sigma weight residual 20.00 -4.89 24.89 1 8.00e+00 1.56e-02 1.39e+01 ... (remaining 8456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2068 0.089 - 0.178: 164 0.178 - 0.267: 3 0.267 - 0.356: 1 0.356 - 0.446: 1 Chirality restraints: 2237 Sorted by residual: chirality pdb=" P U D 2 " pdb=" OP1 U D 2 " pdb=" OP2 U D 2 " pdb=" O5' U D 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CB ILE A 6 " pdb=" CA ILE A 6 " pdb=" CG1 ILE A 6 " pdb=" CG2 ILE A 6 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' U D 2 " pdb=" C4' U D 2 " pdb=" O3' U D 2 " pdb=" C2' U D 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2234 not shown) Planarity restraints: 2462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 61 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO B 62 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 173 " -0.014 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP B 173 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 173 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 173 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 173 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 173 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 173 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 490 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 491 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 491 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 491 " -0.026 5.00e-02 4.00e+02 ... (remaining 2459 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1431 2.75 - 3.28: 13737 3.28 - 3.82: 22578 3.82 - 4.36: 25675 4.36 - 4.90: 45458 Nonbonded interactions: 108879 Sorted by model distance: nonbonded pdb=" O SER C 470 " pdb=" OG SER C 473 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 411 " pdb=" OG1 THR A 469 " model vdw 2.223 3.040 nonbonded pdb=" N GLU A 226 " pdb=" OE1 GLU A 226 " model vdw 2.223 3.120 nonbonded pdb=" O HIS B 344 " pdb=" ND1 HIS B 344 " model vdw 2.225 3.120 nonbonded pdb=" O LEU A 111 " pdb=" OG SER A 114 " model vdw 2.235 3.040 ... (remaining 108874 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 6 through 596) selection = (chain 'B' and resid 6 through 596) selection = (chain 'C' and resid 6 through 596) } ncs_group { reference = (chain 'D' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name O4 or name C5 or name C6 )) or resid 2 thr \ ough 3)) selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.230 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.390 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.003 0.036 13911 Z= 0.144 Angle : 0.583 7.714 18945 Z= 0.306 Chirality : 0.045 0.446 2237 Planarity : 0.004 0.094 2462 Dihedral : 18.728 174.171 5213 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 0.57 % Allowed : 35.72 % Favored : 63.71 % 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: 0.35 (0.21), residues: 1776 helix: 1.68 (0.22), residues: 551 sheet: -0.04 (0.24), residues: 426 loop : -0.58 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 173 HIS 0.001 0.001 HIS A 409 PHE 0.015 0.001 PHE C 531 TYR 0.012 0.001 TYR B 80 ARG 0.008 0.000 ARG C 517 Details of bonding type rmsd hydrogen bonds : bond 0.13016 ( 676) hydrogen bonds : angle 5.77728 ( 1881) covalent geometry : bond 0.00298 (13911) covalent geometry : angle 0.58289 (18945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 1.733 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 189 average time/residue: 0.2755 time to fit residues: 78.2936 Evaluate side-chains 178 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 466 ASN Chi-restraints excluded: chain B residue 189 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN B 61 ASN B 308 GLN C 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115783 restraints weight = 17677.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116436 restraints weight = 13538.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117785 restraints weight = 11889.572| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13911 Z= 0.222 Angle : 0.611 6.523 18945 Z= 0.313 Chirality : 0.046 0.273 2237 Planarity : 0.005 0.062 2462 Dihedral : 10.462 173.770 2146 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 6.11 % Allowed : 32.24 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.21), residues: 1776 helix: 1.34 (0.22), residues: 565 sheet: -0.07 (0.24), residues: 435 loop : -0.55 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 173 HIS 0.003 0.001 HIS A 409 PHE 0.015 0.002 PHE A 416 TYR 0.017 0.002 TYR C 411 ARG 0.006 0.001 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 676) hydrogen bonds : angle 5.02115 ( 1881) covalent geometry : bond 0.00526 (13911) covalent geometry : angle 0.61124 (18945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 179 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7480 (ptp90) cc_final: 0.7242 (ptp-110) REVERT: A 420 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 574 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8393 (mm) REVERT: B 312 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6164 (ttp80) REVERT: C 53 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9203 (tp) REVERT: C 202 ILE cc_start: 0.8592 (mm) cc_final: 0.8257 (mm) REVERT: C 379 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8247 (m) outliers start: 86 outliers final: 50 residues processed: 244 average time/residue: 0.2956 time to fit residues: 110.1546 Evaluate side-chains 218 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 72 optimal weight: 0.8980 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN B 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118597 restraints weight = 17561.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119014 restraints weight = 13717.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120808 restraints weight = 11834.355| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13911 Z= 0.158 Angle : 0.559 7.061 18945 Z= 0.286 Chirality : 0.044 0.272 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.247 174.184 2141 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.56 % Favored : 95.27 % Rotamer: Outliers : 6.61 % Allowed : 31.82 % Favored : 61.58 % 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: 0.28 (0.21), residues: 1776 helix: 1.45 (0.22), residues: 563 sheet: -0.03 (0.24), residues: 435 loop : -0.56 (0.25), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 173 HIS 0.002 0.000 HIS B 344 PHE 0.013 0.001 PHE B 416 TYR 0.012 0.001 TYR C 45 ARG 0.006 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 676) hydrogen bonds : angle 4.79293 ( 1881) covalent geometry : bond 0.00372 (13911) covalent geometry : angle 0.55862 (18945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 184 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7408 (ptp90) cc_final: 0.7111 (ptp-110) REVERT: A 420 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 473 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 54 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.9105 (p) REVERT: C 202 ILE cc_start: 0.8486 (mm) cc_final: 0.8008 (mm) REVERT: C 379 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8201 (m) REVERT: C 534 MET cc_start: 0.7180 (tmm) cc_final: 0.6968 (tmm) outliers start: 93 outliers final: 56 residues processed: 252 average time/residue: 0.2299 time to fit residues: 88.0173 Evaluate side-chains 228 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 109 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126046 restraints weight = 17152.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125205 restraints weight = 13793.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125908 restraints weight = 12512.247| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13911 Z= 0.135 Angle : 0.547 7.735 18945 Z= 0.278 Chirality : 0.044 0.270 2237 Planarity : 0.004 0.047 2462 Dihedral : 10.147 174.746 2141 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 7.39 % Allowed : 30.89 % Favored : 61.72 % 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: 0.32 (0.21), residues: 1776 helix: 1.53 (0.22), residues: 563 sheet: -0.05 (0.24), residues: 437 loop : -0.54 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 173 HIS 0.003 0.000 HIS B 344 PHE 0.013 0.001 PHE B 416 TYR 0.011 0.001 TYR C 45 ARG 0.005 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 676) hydrogen bonds : angle 4.66987 ( 1881) covalent geometry : bond 0.00315 (13911) covalent geometry : angle 0.54660 (18945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 181 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 222 GLN cc_start: 0.7720 (pp30) cc_final: 0.7116 (pt0) REVERT: B 292 ILE cc_start: 0.3445 (OUTLIER) cc_final: 0.3223 (mp) REVERT: B 473 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8593 (p) REVERT: C 53 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9195 (tp) REVERT: C 202 ILE cc_start: 0.8424 (mm) cc_final: 0.8148 (mm) REVERT: C 344 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5804 (t70) REVERT: C 379 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8215 (m) outliers start: 104 outliers final: 71 residues processed: 259 average time/residue: 0.2175 time to fit residues: 86.2783 Evaluate side-chains 245 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 168 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115096 restraints weight = 17848.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115481 restraints weight = 14240.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117199 restraints weight = 12533.257| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13911 Z= 0.199 Angle : 0.597 7.887 18945 Z= 0.303 Chirality : 0.045 0.271 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.166 174.153 2141 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 7.67 % Allowed : 30.68 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.21), residues: 1776 helix: 1.44 (0.22), residues: 564 sheet: -0.06 (0.24), residues: 436 loop : -0.61 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 173 HIS 0.003 0.001 HIS A 409 PHE 0.016 0.002 PHE B 416 TYR 0.017 0.001 TYR C 411 ARG 0.008 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 676) hydrogen bonds : angle 4.74387 ( 1881) covalent geometry : bond 0.00477 (13911) covalent geometry : angle 0.59707 (18945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 176 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: B 222 GLN cc_start: 0.7790 (pp30) cc_final: 0.7193 (pt0) REVERT: B 292 ILE cc_start: 0.3671 (OUTLIER) cc_final: 0.3414 (mp) REVERT: B 312 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6273 (ttp80) REVERT: B 355 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6723 (mp) REVERT: B 473 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8639 (p) REVERT: C 53 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9183 (tp) REVERT: C 202 ILE cc_start: 0.8413 (mm) cc_final: 0.8158 (mm) REVERT: C 344 HIS cc_start: 0.6793 (OUTLIER) cc_final: 0.5878 (t70) REVERT: C 534 MET cc_start: 0.7295 (tmm) cc_final: 0.7069 (tmm) outliers start: 108 outliers final: 85 residues processed: 259 average time/residue: 0.2334 time to fit residues: 90.7674 Evaluate side-chains 264 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 172 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 3 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116112 restraints weight = 17758.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116736 restraints weight = 14338.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118371 restraints weight = 12153.963| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13911 Z= 0.186 Angle : 0.599 12.559 18945 Z= 0.301 Chirality : 0.045 0.329 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.124 174.522 2141 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 7.95 % Allowed : 29.90 % Favored : 62.14 % 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: 0.20 (0.21), residues: 1776 helix: 1.42 (0.22), residues: 564 sheet: -0.12 (0.24), residues: 436 loop : -0.61 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 173 HIS 0.002 0.001 HIS B 344 PHE 0.017 0.001 PHE B 416 TYR 0.015 0.001 TYR C 411 ARG 0.008 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 676) hydrogen bonds : angle 4.72407 ( 1881) covalent geometry : bond 0.00444 (13911) covalent geometry : angle 0.59934 (18945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 184 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 222 GLN cc_start: 0.7763 (pp30) cc_final: 0.7155 (pt0) REVERT: B 292 ILE cc_start: 0.3656 (OUTLIER) cc_final: 0.3436 (mp) REVERT: B 312 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6235 (ttp80) REVERT: B 355 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6731 (mp) REVERT: B 473 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8601 (p) REVERT: C 8 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5389 (mp0) REVERT: C 53 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9178 (tp) REVERT: C 202 ILE cc_start: 0.8402 (mm) cc_final: 0.8141 (mm) REVERT: C 344 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5868 (t70) REVERT: C 379 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8291 (m) REVERT: C 534 MET cc_start: 0.7330 (tmm) cc_final: 0.7037 (tmm) REVERT: C 550 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 112 outliers final: 88 residues processed: 272 average time/residue: 0.2234 time to fit residues: 91.5657 Evaluate side-chains 269 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 171 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117783 restraints weight = 17779.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118369 restraints weight = 13879.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119861 restraints weight = 12709.921| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13911 Z= 0.127 Angle : 0.567 10.790 18945 Z= 0.286 Chirality : 0.044 0.269 2237 Planarity : 0.004 0.068 2462 Dihedral : 9.986 175.180 2141 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 6.96 % Allowed : 31.61 % Favored : 61.43 % 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: 0.34 (0.21), residues: 1776 helix: 1.54 (0.22), residues: 564 sheet: 0.04 (0.24), residues: 427 loop : -0.59 (0.25), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 173 HIS 0.002 0.000 HIS B 344 PHE 0.016 0.001 PHE B 416 TYR 0.011 0.001 TYR A 411 ARG 0.016 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 676) hydrogen bonds : angle 4.56475 ( 1881) covalent geometry : bond 0.00294 (13911) covalent geometry : angle 0.56722 (18945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6881 (t80) REVERT: A 420 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 11 PHE cc_start: 0.4611 (m-80) cc_final: 0.4347 (m-80) REVERT: B 61 ASN cc_start: 0.8063 (m-40) cc_final: 0.7004 (p0) REVERT: B 222 GLN cc_start: 0.7724 (pp30) cc_final: 0.7101 (pt0) REVERT: B 292 ILE cc_start: 0.3656 (OUTLIER) cc_final: 0.3434 (mp) REVERT: B 312 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6296 (ttp80) REVERT: B 473 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8571 (p) REVERT: C 53 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9168 (tp) REVERT: C 202 ILE cc_start: 0.8336 (mm) cc_final: 0.8036 (mm) REVERT: C 344 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.5840 (t70) REVERT: C 379 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8243 (m) REVERT: C 534 MET cc_start: 0.7288 (tmm) cc_final: 0.6997 (tmm) outliers start: 98 outliers final: 75 residues processed: 265 average time/residue: 0.2348 time to fit residues: 94.1259 Evaluate side-chains 259 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 176 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 152 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117982 restraints weight = 17595.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118506 restraints weight = 13444.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119726 restraints weight = 11829.664| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13911 Z= 0.224 Angle : 0.634 10.725 18945 Z= 0.320 Chirality : 0.047 0.359 2237 Planarity : 0.004 0.047 2462 Dihedral : 10.062 174.616 2141 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 7.53 % Allowed : 30.61 % Favored : 61.86 % 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: 0.20 (0.21), residues: 1776 helix: 1.34 (0.22), residues: 565 sheet: -0.05 (0.24), residues: 435 loop : -0.59 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 173 HIS 0.003 0.001 HIS A 409 PHE 0.016 0.002 PHE C 531 TYR 0.018 0.002 TYR C 411 ARG 0.013 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 676) hydrogen bonds : angle 4.75224 ( 1881) covalent geometry : bond 0.00538 (13911) covalent geometry : angle 0.63363 (18945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 173 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 420 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 11 PHE cc_start: 0.4985 (m-80) cc_final: 0.4689 (m-80) REVERT: B 61 ASN cc_start: 0.8007 (m-40) cc_final: 0.6935 (p0) REVERT: B 222 GLN cc_start: 0.7793 (pp30) cc_final: 0.7193 (pt0) REVERT: B 276 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: B 292 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3492 (mp) REVERT: B 312 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6267 (ttp80) REVERT: B 473 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 53 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9230 (tp) REVERT: C 202 ILE cc_start: 0.8383 (mm) cc_final: 0.8123 (mm) REVERT: C 344 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.5877 (t70) REVERT: C 534 MET cc_start: 0.7247 (tmm) cc_final: 0.7001 (tmm) outliers start: 106 outliers final: 86 residues processed: 259 average time/residue: 0.2367 time to fit residues: 91.2742 Evaluate side-chains 263 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 169 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 577 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121290 restraints weight = 17274.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123470 restraints weight = 12704.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124811 restraints weight = 10904.317| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13911 Z= 0.153 Angle : 0.595 12.509 18945 Z= 0.299 Chirality : 0.045 0.296 2237 Planarity : 0.004 0.047 2462 Dihedral : 9.947 175.273 2141 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 7.10 % Allowed : 30.82 % Favored : 62.07 % 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: 0.26 (0.21), residues: 1776 helix: 1.43 (0.22), residues: 564 sheet: -0.09 (0.24), residues: 440 loop : -0.53 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 173 HIS 0.002 0.000 HIS B 344 PHE 0.019 0.001 PHE C 531 TYR 0.012 0.001 TYR C 45 ARG 0.010 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 676) hydrogen bonds : angle 4.63626 ( 1881) covalent geometry : bond 0.00363 (13911) covalent geometry : angle 0.59490 (18945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 178 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 420 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 11 PHE cc_start: 0.4692 (m-80) cc_final: 0.4453 (m-80) REVERT: B 61 ASN cc_start: 0.7937 (m-40) cc_final: 0.6878 (p0) REVERT: B 222 GLN cc_start: 0.7707 (pp30) cc_final: 0.7106 (pt0) REVERT: B 292 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3462 (mp) REVERT: B 312 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6233 (ttp80) REVERT: B 473 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (p) REVERT: C 53 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9250 (tp) REVERT: C 202 ILE cc_start: 0.8343 (mm) cc_final: 0.8060 (mm) REVERT: C 344 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.5865 (t70) REVERT: C 379 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8300 (m) REVERT: C 534 MET cc_start: 0.7216 (tmm) cc_final: 0.6954 (tmm) outliers start: 100 outliers final: 84 residues processed: 257 average time/residue: 0.2225 time to fit residues: 87.2550 Evaluate side-chains 265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 173 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 117 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120864 restraints weight = 17291.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122749 restraints weight = 12570.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124433 restraints weight = 10439.901| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13911 Z= 0.262 Angle : 0.679 12.643 18945 Z= 0.344 Chirality : 0.048 0.302 2237 Planarity : 0.005 0.047 2462 Dihedral : 10.076 174.818 2141 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Rotamer: Outliers : 7.39 % Allowed : 30.54 % Favored : 62.07 % 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: 0.07 (0.21), residues: 1776 helix: 1.22 (0.22), residues: 564 sheet: -0.14 (0.24), residues: 435 loop : -0.63 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 173 HIS 0.003 0.001 HIS A 409 PHE 0.018 0.002 PHE B 531 TYR 0.021 0.002 TYR C 411 ARG 0.010 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 676) hydrogen bonds : angle 4.85932 ( 1881) covalent geometry : bond 0.00629 (13911) covalent geometry : angle 0.67885 (18945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 173 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6996 (t80) REVERT: A 329 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6964 (mtm110) REVERT: A 337 ARG cc_start: 0.7831 (mtp85) cc_final: 0.6993 (mtp85) REVERT: A 420 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 523 ASP cc_start: 0.7615 (m-30) cc_final: 0.7377 (m-30) REVERT: B 61 ASN cc_start: 0.7943 (m-40) cc_final: 0.6893 (p0) REVERT: B 276 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5973 (m-80) REVERT: B 292 ILE cc_start: 0.3653 (OUTLIER) cc_final: 0.3422 (mp) REVERT: B 312 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6233 (ttp80) REVERT: C 53 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9243 (tp) REVERT: C 202 ILE cc_start: 0.8405 (mm) cc_final: 0.8149 (mm) REVERT: C 344 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.5942 (t70) REVERT: C 534 MET cc_start: 0.7306 (tmm) cc_final: 0.7037 (tmm) outliers start: 104 outliers final: 87 residues processed: 257 average time/residue: 0.2570 time to fit residues: 99.5507 Evaluate side-chains 263 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 169 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117602 restraints weight = 17719.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118404 restraints weight = 13430.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119983 restraints weight = 11553.214| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13911 Z= 0.151 Angle : 0.611 11.092 18945 Z= 0.309 Chirality : 0.045 0.270 2237 Planarity : 0.004 0.047 2462 Dihedral : 9.930 175.310 2141 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 6.89 % Allowed : 31.18 % Favored : 61.93 % 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: 0.19 (0.21), residues: 1776 helix: 1.35 (0.22), residues: 564 sheet: -0.15 (0.24), residues: 440 loop : -0.53 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP B 173 HIS 0.002 0.000 HIS B 344 PHE 0.019 0.001 PHE C 531 TYR 0.012 0.001 TYR A 411 ARG 0.010 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 676) hydrogen bonds : angle 4.67657 ( 1881) covalent geometry : bond 0.00359 (13911) covalent geometry : angle 0.61069 (18945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4242.97 seconds wall clock time: 75 minutes 35.63 seconds (4535.63 seconds total)