Starting phenix.real_space_refine on Tue Apr 29 01:45:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzy_8942/04_2025/6dzy_8942_neut.cif" } resolution = 4.1 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= 0.003 sd= 1.383 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 99 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5117 2.51 5 N 1249 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4282 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HJM': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.78, per 1000 atoms: 0.61 Number of scatterers: 7842 At special positions: 0 Unit cell: (90.828, 103.356, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1436 8.00 N 1249 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 111 " distance=2.03 Simple disulfide: pdb=" SG CYS V 172 " - pdb=" SG CYS V 237 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 208 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 834.9 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 48.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.646A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.965A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 4.403A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.959A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 191 removed outlier: 4.269A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 272 removed outlier: 3.784A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.632A pdb=" N GLY A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 302 removed outlier: 4.060A pdb=" N ARG A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.043A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.594A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 391 removed outlier: 3.643A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 417 removed outlier: 3.506A pdb=" N TYR A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 454 removed outlier: 3.702A pdb=" N PHE A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.624A pdb=" N VAL A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.704A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.571A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.885A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.666A pdb=" N LEU A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.797A pdb=" N ILE A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.582A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'H' and resid 82 through 85 removed outlier: 3.886A pdb=" N GLY H 85 " --> pdb=" O LYS H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 85' Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'V' and resid 43 through 47 removed outlier: 4.101A pdb=" N TYR V 47 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 80 removed outlier: 3.678A pdb=" N LYS V 80 " --> pdb=" O GLN V 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 77 through 80' Processing helix chain 'V' and resid 89 through 91 No H-bonds generated for 'chain 'V' and resid 89 through 91' Processing helix chain 'V' and resid 102 through 106 Processing helix chain 'V' and resid 228 through 232 Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.652A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER H 44 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 29 through 30 removed outlier: 3.803A pdb=" N THR H 137 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 116 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.668A pdb=" N THR H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 25 removed outlier: 3.604A pdb=" N ALA L 39 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 41 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE L 95 " --> pdb=" O CYS L 43 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER L 89 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.963A pdb=" N GLU L 129 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 128 " --> pdb=" O ALA L 108 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE L 111 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.963A pdb=" N GLU L 129 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 128 " --> pdb=" O ALA L 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.738A pdb=" N ASN L 51 " --> pdb=" O ILE L 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 18 through 21 removed outlier: 3.562A pdb=" N THR V 86 " --> pdb=" O TYR V 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 25 through 26 removed outlier: 6.519A pdb=" N GLU V 25 " --> pdb=" O THR V 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL V 52 " --> pdb=" O TYR V 110 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP V 51 " --> pdb=" O ILE V 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 25 through 26 removed outlier: 6.519A pdb=" N GLU V 25 " --> pdb=" O THR V 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR V 123 " --> pdb=" O ARG V 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 153 through 155 removed outlier: 11.889A pdb=" N CYS V 172 " --> pdb=" O THR V 223 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N THR V 223 " --> pdb=" O CYS V 172 " (cutoff:3.500A) removed outlier: 11.846A pdb=" N ALA V 174 " --> pdb=" O THR V 221 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N THR V 221 " --> pdb=" O ALA V 174 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N GLN V 176 " --> pdb=" O ASP V 219 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP V 219 " --> pdb=" O GLN V 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 184 through 185 removed outlier: 6.744A pdb=" N TRP V 184 " --> pdb=" O LEU V 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 234 through 235 removed outlier: 3.573A pdb=" N THR V 251 " --> pdb=" O TYR V 235 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1194 1.27 - 1.41: 2235 1.41 - 1.54: 4523 1.54 - 1.68: 58 1.68 - 1.82: 59 Bond restraints: 8069 Sorted by residual: bond pdb=" C VAL A 367 " pdb=" N ASN A 368 " ideal model delta sigma weight residual 1.335 1.454 -0.119 1.31e-02 5.83e+03 8.25e+01 bond pdb=" C ASN A 208 " pdb=" O ASN A 208 " ideal model delta sigma weight residual 1.235 1.137 0.098 1.26e-02 6.30e+03 6.07e+01 bond pdb=" C PRO A 571 " pdb=" N TYR A 572 " ideal model delta sigma weight residual 1.333 1.221 0.112 1.45e-02 4.76e+03 5.92e+01 bond pdb=" C ASN A 368 " pdb=" N CYS A 369 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.43e-02 4.89e+03 5.21e+01 bond pdb=" C1 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.463 1.568 -0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 10946 5.31 - 10.61: 34 10.61 - 15.92: 3 15.92 - 21.23: 0 21.23 - 26.53: 1 Bond angle restraints: 10984 Sorted by residual: angle pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta sigma weight residual 111.62 138.15 -26.53 1.43e+00 4.89e-01 3.44e+02 angle pdb=" C TYR A 176 " pdb=" N ASN A 177 " pdb=" CA ASN A 177 " ideal model delta sigma weight residual 120.29 133.18 -12.89 1.42e+00 4.96e-01 8.23e+01 angle pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" C TYR V 119 " ideal model delta sigma weight residual 111.30 99.18 12.12 1.36e+00 5.41e-01 7.94e+01 angle pdb=" N TYR A 176 " pdb=" CA TYR A 176 " pdb=" C TYR A 176 " ideal model delta sigma weight residual 111.36 120.93 -9.57 1.09e+00 8.42e-01 7.70e+01 angle pdb=" C SER A 532 " pdb=" N PRO A 533 " pdb=" CA PRO A 533 " ideal model delta sigma weight residual 121.00 130.13 -9.13 1.16e+00 7.43e-01 6.19e+01 ... (remaining 10979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 4586 22.45 - 44.90: 89 44.90 - 67.35: 19 67.35 - 89.79: 9 89.79 - 112.24: 13 Dihedral angle restraints: 4716 sinusoidal: 1870 harmonic: 2846 Sorted by residual: dihedral pdb=" N TYR V 119 " pdb=" C TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta harmonic sigma weight residual 122.80 151.95 -29.15 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 38.41 -38.41 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" C TYR V 119 " pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 4713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 1206 0.211 - 0.422: 6 0.422 - 0.633: 2 0.633 - 0.844: 0 0.844 - 1.055: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" CA TYR V 119 " pdb=" N TYR V 119 " pdb=" C TYR V 119 " pdb=" CB TYR V 119 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" N1 HJM A 701 " pdb=" C1 HJM A 701 " pdb=" C7 HJM A 701 " pdb=" C9 HJM A 701 " both_signs ideal model delta sigma weight residual False 1.76 2.30 -0.55 2.00e-01 2.50e+01 7.43e+00 ... (remaining 1212 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.35e+02 pdb=" C7 NAG B 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O HJM A 701 " 0.166 2.00e-02 2.50e+03 8.51e-02 2.17e+02 pdb=" C11 HJM A 701 " 0.113 2.00e-02 2.50e+03 pdb=" C12 HJM A 701 " -0.117 2.00e-02 2.50e+03 pdb=" C13 HJM A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C15 HJM A 701 " -0.043 2.00e-02 2.50e+03 pdb=" C16 HJM A 701 " -0.127 2.00e-02 2.50e+03 pdb=" C17 HJM A 701 " -0.021 2.00e-02 2.50e+03 pdb=" C18 HJM A 701 " -0.029 2.00e-02 2.50e+03 pdb=" C19 HJM A 701 " -0.039 2.00e-02 2.50e+03 pdb=" C2 HJM A 701 " 0.054 2.00e-02 2.50e+03 pdb=" C8 HJM A 701 " 0.085 2.00e-02 2.50e+03 pdb=" N2 HJM A 701 " -0.045 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.79: 1967 2.79 - 3.49: 10494 3.49 - 4.20: 18630 4.20 - 4.90: 32250 Nonbonded interactions: 63344 Sorted by model distance: nonbonded pdb=" O TRP A 220 " pdb=" CG2 VAL V 116 " model vdw 1.386 3.460 nonbonded pdb=" CD1 ILE A 327 " pdb=" CE2 PHE A 551 " model vdw 1.638 3.760 nonbonded pdb=" CB PRO V 118 " pdb=" CD1 TYR V 120 " model vdw 1.909 3.740 nonbonded pdb=" OE1 GLU A 494 " pdb=" O2B LMT A 702 " model vdw 2.093 3.040 nonbonded pdb=" O GLU A 229 " pdb=" OG1 THR A 233 " model vdw 2.126 3.040 ... (remaining 63339 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 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 : 0.006 0.255 8076 Z= 0.358 Angle : 0.924 26.534 11000 Z= 0.538 Chirality : 0.064 1.055 1215 Planarity : 0.013 0.298 1354 Dihedral : 12.392 112.243 2897 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 1.32 % Allowed : 0.60 % Favored : 98.07 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.99 (0.24), residues: 978 helix: -2.35 (0.21), residues: 357 sheet: -2.11 (0.35), residues: 157 loop : -1.46 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.006 0.001 HIS A 235 PHE 0.014 0.002 PHE A 213 TYR 0.017 0.001 TYR A 176 ARG 0.003 0.001 ARG V 245 Details of bonding type rmsd link_NAG-ASN : bond 0.25458 ( 1) link_NAG-ASN : angle 17.49589 ( 3) link_BETA1-4 : bond 0.00592 ( 1) link_BETA1-4 : angle 2.11207 ( 3) hydrogen bonds : bond 0.29693 ( 349) hydrogen bonds : angle 9.62099 ( 954) SS BOND : bond 0.00281 ( 5) SS BOND : angle 0.59811 ( 10) covalent geometry : bond 0.00578 ( 8069) covalent geometry : angle 0.87772 (10984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 471 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.8792 (p) cc_final: 0.8538 (t) REVERT: A 82 TRP cc_start: 0.5796 (m-10) cc_final: 0.5371 (m-10) REVERT: A 121 TYR cc_start: 0.9167 (t80) cc_final: 0.8563 (t80) REVERT: A 158 PHE cc_start: 0.7206 (m-80) cc_final: 0.6870 (m-80) REVERT: A 184 LEU cc_start: 0.9093 (tp) cc_final: 0.8627 (tp) REVERT: A 189 SER cc_start: 0.9611 (m) cc_final: 0.9332 (p) REVERT: A 195 LEU cc_start: 0.8511 (mt) cc_final: 0.8095 (mt) REVERT: A 197 TRP cc_start: 0.8024 (m-10) cc_final: 0.7629 (m-10) REVERT: A 268 PHE cc_start: 0.8591 (m-80) cc_final: 0.8385 (m-80) REVERT: A 326 TRP cc_start: 0.8560 (m100) cc_final: 0.8295 (m-10) REVERT: A 333 ILE cc_start: 0.9162 (pt) cc_final: 0.8877 (pt) REVERT: A 369 CYS cc_start: 0.9027 (m) cc_final: 0.8764 (m) REVERT: A 386 MET cc_start: 0.7877 (mmm) cc_final: 0.7651 (mmm) REVERT: A 390 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7481 (mtt180) REVERT: A 410 TYR cc_start: 0.8215 (t80) cc_final: 0.7887 (t80) REVERT: A 417 MET cc_start: 0.8004 (mtm) cc_final: 0.7641 (mtm) REVERT: A 422 PHE cc_start: 0.7805 (t80) cc_final: 0.7379 (t80) REVERT: A 460 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7340 (ttpt) REVERT: A 464 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7874 (ttm110) REVERT: A 478 LEU cc_start: 0.8702 (tp) cc_final: 0.8410 (tp) REVERT: A 538 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7504 (ttt-90) REVERT: A 549 LEU cc_start: 0.9293 (mp) cc_final: 0.8952 (pp) REVERT: A 555 SER cc_start: 0.8248 (p) cc_final: 0.8005 (p) REVERT: A 570 TYR cc_start: 0.6643 (m-10) cc_final: 0.6019 (m-80) REVERT: A 592 TYR cc_start: 0.7948 (t80) cc_final: 0.7717 (t80) REVERT: A 593 ILE cc_start: 0.8339 (mt) cc_final: 0.8070 (mt) REVERT: A 597 LEU cc_start: 0.8210 (mt) cc_final: 0.7917 (tt) REVERT: H 21 VAL cc_start: 0.8059 (t) cc_final: 0.7641 (t) REVERT: L 71 LEU cc_start: 0.8324 (mt) cc_final: 0.8110 (mt) REVERT: L 72 ILE cc_start: 0.8701 (mm) cc_final: 0.8054 (tp) REVERT: L 83 PRO cc_start: 0.8309 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: L 121 THR cc_start: 0.7359 (p) cc_final: 0.6575 (m) REVERT: V 43 THR cc_start: 0.8404 (m) cc_final: 0.8075 (t) REVERT: V 47 TYR cc_start: 0.4447 (p90) cc_final: 0.2915 (p90) REVERT: V 56 HIS cc_start: 0.6481 (t70) cc_final: 0.6070 (p-80) REVERT: V 93 THR cc_start: 0.8861 (m) cc_final: 0.8499 (p) REVERT: V 195 LEU cc_start: 0.8989 (tp) cc_final: 0.8503 (tp) REVERT: V 236 TYR cc_start: 0.7410 (m-80) cc_final: 0.7187 (m-80) REVERT: V 241 TYR cc_start: 0.8559 (t80) cc_final: 0.7786 (t80) outliers start: 11 outliers final: 8 residues processed: 478 average time/residue: 0.1972 time to fit residues: 125.2566 Evaluate side-chains 353 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 211 ASN A 235 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN H 58 GLN L 61 GLN V 239 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.177523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153320 restraints weight = 15501.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158972 restraints weight = 9255.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163121 restraints weight = 6054.389| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8076 Z= 0.173 Angle : 0.737 10.815 11000 Z= 0.374 Chirality : 0.049 0.289 1215 Planarity : 0.006 0.109 1354 Dihedral : 9.432 68.459 1202 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.91 % Favored : 94.99 % Rotamer: Outliers : 0.24 % Allowed : 2.29 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.25), residues: 978 helix: -0.59 (0.24), residues: 377 sheet: -1.03 (0.37), residues: 160 loop : -1.38 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP V 62 HIS 0.005 0.001 HIS A 143 PHE 0.026 0.002 PHE V 220 TYR 0.029 0.002 TYR A 176 ARG 0.004 0.001 ARG V 117 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 1) link_NAG-ASN : angle 8.52796 ( 3) link_BETA1-4 : bond 0.00133 ( 1) link_BETA1-4 : angle 2.52293 ( 3) hydrogen bonds : bond 0.05913 ( 349) hydrogen bonds : angle 5.80111 ( 954) SS BOND : bond 0.00809 ( 5) SS BOND : angle 1.83635 ( 10) covalent geometry : bond 0.00372 ( 8069) covalent geometry : angle 0.72051 (10984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 400 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.8888 (p) cc_final: 0.8603 (t) REVERT: A 82 TRP cc_start: 0.5484 (m-10) cc_final: 0.5253 (m-10) REVERT: A 84 LYS cc_start: 0.8396 (mptt) cc_final: 0.7876 (tptp) REVERT: A 121 TYR cc_start: 0.9144 (t80) cc_final: 0.8709 (t80) REVERT: A 171 TYR cc_start: 0.8783 (m-80) cc_final: 0.8562 (m-80) REVERT: A 189 SER cc_start: 0.9592 (m) cc_final: 0.9358 (p) REVERT: A 195 LEU cc_start: 0.8649 (mt) cc_final: 0.8057 (mt) REVERT: A 197 TRP cc_start: 0.8535 (m-10) cc_final: 0.8071 (m-10) REVERT: A 298 ARG cc_start: 0.8089 (tpm170) cc_final: 0.7705 (tpp-160) REVERT: A 316 ASN cc_start: 0.7554 (t0) cc_final: 0.7236 (t0) REVERT: A 370 MET cc_start: 0.7257 (mtm) cc_final: 0.7024 (mmm) REVERT: A 385 TYR cc_start: 0.7357 (t80) cc_final: 0.7000 (t80) REVERT: A 390 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8084 (mtt180) REVERT: A 393 ASP cc_start: 0.8661 (t70) cc_final: 0.8460 (t70) REVERT: A 417 MET cc_start: 0.8191 (mtm) cc_final: 0.7619 (mtm) REVERT: A 453 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8527 (mm-30) REVERT: A 460 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7529 (ttpt) REVERT: A 512 VAL cc_start: 0.8930 (p) cc_final: 0.8724 (p) REVERT: A 538 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7237 (ttt-90) REVERT: A 567 GLN cc_start: 0.9088 (pm20) cc_final: 0.8862 (pm20) REVERT: A 581 ILE cc_start: 0.8491 (mt) cc_final: 0.8288 (mt) REVERT: A 592 TYR cc_start: 0.8306 (t80) cc_final: 0.7353 (t80) REVERT: A 593 ILE cc_start: 0.8610 (mt) cc_final: 0.8348 (mt) REVERT: H 22 GLN cc_start: 0.6555 (mp10) cc_final: 0.6344 (mp10) REVERT: H 76 ASP cc_start: 0.8596 (t0) cc_final: 0.8181 (t0) REVERT: H 120 TYR cc_start: 0.7266 (m-80) cc_final: 0.6573 (m-80) REVERT: L 114 GLN cc_start: 0.7982 (pm20) cc_final: 0.7425 (pm20) REVERT: V 21 GLN cc_start: 0.6306 (mt0) cc_final: 0.5628 (mt0) REVERT: V 37 CYS cc_start: 0.4399 (p) cc_final: 0.3756 (p) REVERT: V 51 TRP cc_start: 0.8229 (m100) cc_final: 0.7793 (m100) REVERT: V 56 HIS cc_start: 0.6459 (t70) cc_final: 0.6058 (p-80) REVERT: V 62 TRP cc_start: 0.8722 (t60) cc_final: 0.8397 (t60) REVERT: V 92 THR cc_start: 0.8673 (p) cc_final: 0.8186 (t) REVERT: V 93 THR cc_start: 0.8282 (m) cc_final: 0.7924 (p) REVERT: V 105 ASP cc_start: 0.8835 (m-30) cc_final: 0.8493 (m-30) REVERT: V 176 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7485 (mm-40) REVERT: V 184 TRP cc_start: 0.9133 (m100) cc_final: 0.8534 (m100) REVERT: V 246 THR cc_start: 0.8126 (p) cc_final: 0.7706 (p) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.1721 time to fit residues: 95.4522 Evaluate side-chains 328 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS A 368 ASN A 391 ASN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN V 69 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.174932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151114 restraints weight = 14954.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156869 restraints weight = 8677.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161069 restraints weight = 5577.135| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8076 Z= 0.138 Angle : 0.662 11.677 11000 Z= 0.333 Chirality : 0.045 0.345 1215 Planarity : 0.005 0.086 1354 Dihedral : 6.783 46.566 1202 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 0.12 % Allowed : 1.56 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 978 helix: -0.05 (0.25), residues: 382 sheet: -0.95 (0.36), residues: 175 loop : -1.26 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 55 HIS 0.005 0.001 HIS A 240 PHE 0.042 0.002 PHE A 440 TYR 0.020 0.002 TYR A 570 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 1) link_NAG-ASN : angle 5.72412 ( 3) link_BETA1-4 : bond 0.01267 ( 1) link_BETA1-4 : angle 1.70290 ( 3) hydrogen bonds : bond 0.05042 ( 349) hydrogen bonds : angle 5.27736 ( 954) SS BOND : bond 0.00647 ( 5) SS BOND : angle 1.04034 ( 10) covalent geometry : bond 0.00287 ( 8069) covalent geometry : angle 0.65406 (10984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.8987 (p) cc_final: 0.8611 (t) REVERT: A 82 TRP cc_start: 0.5665 (m-10) cc_final: 0.5410 (m-10) REVERT: A 121 TYR cc_start: 0.9113 (t80) cc_final: 0.8641 (t80) REVERT: A 142 TYR cc_start: 0.8567 (t80) cc_final: 0.8296 (t80) REVERT: A 184 LEU cc_start: 0.9049 (tp) cc_final: 0.8696 (tp) REVERT: A 189 SER cc_start: 0.9611 (m) cc_final: 0.9359 (p) REVERT: A 195 LEU cc_start: 0.8718 (mt) cc_final: 0.7847 (mt) REVERT: A 197 TRP cc_start: 0.8642 (m-10) cc_final: 0.7991 (m-10) REVERT: A 284 THR cc_start: 0.8903 (p) cc_final: 0.8692 (p) REVERT: A 298 ARG cc_start: 0.7928 (tpm170) cc_final: 0.7209 (tpp-160) REVERT: A 316 ASN cc_start: 0.7738 (t0) cc_final: 0.7377 (t0) REVERT: A 333 ILE cc_start: 0.9203 (pt) cc_final: 0.8926 (pt) REVERT: A 370 MET cc_start: 0.6655 (mtm) cc_final: 0.6402 (mmm) REVERT: A 385 TYR cc_start: 0.7417 (t80) cc_final: 0.7055 (t80) REVERT: A 410 TYR cc_start: 0.7713 (t80) cc_final: 0.7428 (t80) REVERT: A 453 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 460 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7564 (ttpt) REVERT: A 512 VAL cc_start: 0.8975 (p) cc_final: 0.8751 (p) REVERT: A 538 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7098 (ttt-90) REVERT: A 567 GLN cc_start: 0.9111 (pm20) cc_final: 0.8877 (pm20) REVERT: A 576 ILE cc_start: 0.8090 (tp) cc_final: 0.7839 (tp) REVERT: H 22 GLN cc_start: 0.6741 (mp10) cc_final: 0.6474 (mp10) REVERT: H 76 ASP cc_start: 0.8433 (t0) cc_final: 0.7961 (t0) REVERT: H 120 TYR cc_start: 0.7417 (m-80) cc_final: 0.6276 (m-80) REVERT: H 128 ASP cc_start: 0.8268 (t70) cc_final: 0.7994 (t70) REVERT: L 62 GLN cc_start: 0.6007 (tp40) cc_final: 0.5804 (tp40) REVERT: L 100 HIS cc_start: 0.6808 (m90) cc_final: 0.6351 (m90) REVERT: L 121 THR cc_start: 0.6881 (p) cc_final: 0.5955 (t) REVERT: V 18 GLN cc_start: 0.8541 (mm110) cc_final: 0.8035 (mp10) REVERT: V 21 GLN cc_start: 0.6485 (mt0) cc_final: 0.5934 (mt0) REVERT: V 37 CYS cc_start: 0.4895 (p) cc_final: 0.3350 (p) REVERT: V 47 TYR cc_start: 0.3198 (p90) cc_final: 0.2069 (p90) REVERT: V 48 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5250 (m-10) REVERT: V 51 TRP cc_start: 0.8200 (m100) cc_final: 0.7956 (m100) REVERT: V 56 HIS cc_start: 0.6514 (t70) cc_final: 0.5986 (p-80) REVERT: V 62 TRP cc_start: 0.8885 (t60) cc_final: 0.8468 (t60) REVERT: V 76 ASN cc_start: 0.8052 (t0) cc_final: 0.7331 (p0) REVERT: V 92 THR cc_start: 0.8683 (p) cc_final: 0.8231 (t) REVERT: V 93 THR cc_start: 0.8192 (m) cc_final: 0.7780 (p) REVERT: V 105 ASP cc_start: 0.8782 (m-30) cc_final: 0.8448 (m-30) REVERT: V 173 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7185 (tppt) REVERT: V 176 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7530 (mm-40) REVERT: V 184 TRP cc_start: 0.9221 (m100) cc_final: 0.8503 (m100) REVERT: V 204 TYR cc_start: 0.7042 (t80) cc_final: 0.6808 (t80) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.1724 time to fit residues: 92.4041 Evaluate side-chains 338 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 186 GLN V 187 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134709 restraints weight = 15847.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139673 restraints weight = 9205.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143315 restraints weight = 5981.199| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8076 Z= 0.266 Angle : 0.786 10.367 11000 Z= 0.410 Chirality : 0.048 0.331 1215 Planarity : 0.006 0.074 1354 Dihedral : 6.396 40.934 1202 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 978 helix: 0.04 (0.25), residues: 388 sheet: -0.71 (0.35), residues: 185 loop : -1.36 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 130 HIS 0.004 0.002 HIS A 240 PHE 0.040 0.003 PHE A 440 TYR 0.026 0.003 TYR L 73 ARG 0.008 0.001 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 1) link_NAG-ASN : angle 6.05502 ( 3) link_BETA1-4 : bond 0.01463 ( 1) link_BETA1-4 : angle 1.72296 ( 3) hydrogen bonds : bond 0.05121 ( 349) hydrogen bonds : angle 5.29021 ( 954) SS BOND : bond 0.00510 ( 5) SS BOND : angle 1.22900 ( 10) covalent geometry : bond 0.00569 ( 8069) covalent geometry : angle 0.77908 (10984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9082 (p) cc_final: 0.8833 (p) REVERT: A 121 TYR cc_start: 0.9238 (t80) cc_final: 0.8533 (t80) REVERT: A 184 LEU cc_start: 0.9275 (tp) cc_final: 0.8896 (tp) REVERT: A 205 ASN cc_start: 0.8642 (t0) cc_final: 0.8396 (t0) REVERT: A 245 LEU cc_start: 0.8766 (mm) cc_final: 0.8499 (mm) REVERT: A 248 LEU cc_start: 0.8065 (tp) cc_final: 0.7268 (tt) REVERT: A 284 THR cc_start: 0.8938 (p) cc_final: 0.8733 (p) REVERT: A 316 ASN cc_start: 0.8459 (t0) cc_final: 0.8126 (t0) REVERT: A 328 ASP cc_start: 0.8166 (m-30) cc_final: 0.7881 (m-30) REVERT: A 333 ILE cc_start: 0.9246 (pt) cc_final: 0.8925 (pt) REVERT: A 337 LEU cc_start: 0.9490 (mt) cc_final: 0.9141 (mt) REVERT: A 370 MET cc_start: 0.7083 (mtm) cc_final: 0.6834 (mmm) REVERT: A 385 TYR cc_start: 0.8096 (t80) cc_final: 0.7815 (t80) REVERT: A 405 LEU cc_start: 0.7712 (tt) cc_final: 0.7445 (tp) REVERT: A 410 TYR cc_start: 0.8253 (t80) cc_final: 0.7847 (t80) REVERT: A 447 ILE cc_start: 0.9604 (mt) cc_final: 0.9367 (mt) REVERT: A 453 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8621 (mm-30) REVERT: A 460 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7677 (mtpt) REVERT: A 508 GLU cc_start: 0.9377 (tt0) cc_final: 0.9170 (tt0) REVERT: A 538 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7167 (ttt-90) REVERT: A 567 GLN cc_start: 0.9149 (pm20) cc_final: 0.8830 (pm20) REVERT: A 592 TYR cc_start: 0.8315 (t80) cc_final: 0.7734 (t80) REVERT: A 606 GLU cc_start: 0.8215 (tp30) cc_final: 0.7994 (tp30) REVERT: H 21 VAL cc_start: 0.8374 (t) cc_final: 0.7977 (t) REVERT: H 22 GLN cc_start: 0.6803 (mp10) cc_final: 0.6475 (mp10) REVERT: H 49 SER cc_start: 0.8520 (p) cc_final: 0.8291 (p) REVERT: H 76 ASP cc_start: 0.8771 (t0) cc_final: 0.8488 (t0) REVERT: H 114 PHE cc_start: 0.8983 (m-10) cc_final: 0.8771 (m-10) REVERT: H 120 TYR cc_start: 0.7739 (m-80) cc_final: 0.7209 (m-80) REVERT: H 128 ASP cc_start: 0.8599 (t70) cc_final: 0.7714 (t70) REVERT: H 129 TYR cc_start: 0.8814 (m-10) cc_final: 0.8494 (m-10) REVERT: L 60 PHE cc_start: 0.8354 (m-10) cc_final: 0.7615 (m-10) REVERT: L 71 LEU cc_start: 0.9192 (mt) cc_final: 0.8735 (mt) REVERT: L 83 PRO cc_start: 0.8774 (Cg_exo) cc_final: 0.8299 (Cg_endo) REVERT: L 100 HIS cc_start: 0.7108 (m90) cc_final: 0.6655 (m90) REVERT: L 114 GLN cc_start: 0.7855 (pm20) cc_final: 0.7621 (pm20) REVERT: L 121 THR cc_start: 0.7263 (p) cc_final: 0.6640 (t) REVERT: V 18 GLN cc_start: 0.8506 (mm110) cc_final: 0.7953 (mp10) REVERT: V 20 GLN cc_start: 0.7485 (mm110) cc_final: 0.7193 (mm-40) REVERT: V 21 GLN cc_start: 0.6784 (mt0) cc_final: 0.5836 (mt0) REVERT: V 38 LYS cc_start: 0.7911 (tttt) cc_final: 0.7434 (ttmt) REVERT: V 43 THR cc_start: 0.8141 (m) cc_final: 0.7410 (p) REVERT: V 51 TRP cc_start: 0.8779 (m100) cc_final: 0.8266 (m100) REVERT: V 62 TRP cc_start: 0.8985 (t60) cc_final: 0.8464 (t60) REVERT: V 67 ASN cc_start: 0.8044 (t0) cc_final: 0.7694 (t0) REVERT: V 92 THR cc_start: 0.8683 (p) cc_final: 0.8273 (t) REVERT: V 105 ASP cc_start: 0.8831 (m-30) cc_final: 0.8410 (m-30) REVERT: V 123 TYR cc_start: 0.7265 (m-10) cc_final: 0.6993 (m-10) REVERT: V 151 ILE cc_start: 0.8076 (mt) cc_final: 0.7801 (mt) REVERT: V 176 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7680 (mm-40) REVERT: V 184 TRP cc_start: 0.9156 (m100) cc_final: 0.8550 (m100) REVERT: V 204 TYR cc_start: 0.8055 (t80) cc_final: 0.7583 (t80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1645 time to fit residues: 83.2909 Evaluate side-chains 306 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 391 ASN H 24 GLN L 78 GLN V 65 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.162559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139127 restraints weight = 15193.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144601 restraints weight = 8832.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148529 restraints weight = 5702.606| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8076 Z= 0.136 Angle : 0.676 12.415 11000 Z= 0.340 Chirality : 0.044 0.362 1215 Planarity : 0.005 0.065 1354 Dihedral : 5.857 43.470 1202 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.63 (0.27), residues: 978 helix: 0.51 (0.26), residues: 384 sheet: -0.40 (0.37), residues: 182 loop : -1.25 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 220 HIS 0.006 0.001 HIS A 240 PHE 0.031 0.002 PHE A 440 TYR 0.020 0.002 TYR A 495 ARG 0.004 0.001 ARG H 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 1) link_NAG-ASN : angle 4.79568 ( 3) link_BETA1-4 : bond 0.01037 ( 1) link_BETA1-4 : angle 1.57360 ( 3) hydrogen bonds : bond 0.04517 ( 349) hydrogen bonds : angle 5.06598 ( 954) SS BOND : bond 0.00576 ( 5) SS BOND : angle 1.35786 ( 10) covalent geometry : bond 0.00298 ( 8069) covalent geometry : angle 0.66981 (10984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9149 (p) cc_final: 0.8881 (t) REVERT: A 121 TYR cc_start: 0.9082 (t80) cc_final: 0.8546 (t80) REVERT: A 145 ASN cc_start: 0.7723 (m-40) cc_final: 0.7477 (m-40) REVERT: A 184 LEU cc_start: 0.9192 (tp) cc_final: 0.8834 (tp) REVERT: A 193 ASP cc_start: 0.8170 (p0) cc_final: 0.7690 (m-30) REVERT: A 195 LEU cc_start: 0.8914 (mt) cc_final: 0.8669 (mt) REVERT: A 197 TRP cc_start: 0.9178 (m-10) cc_final: 0.8648 (m-10) REVERT: A 205 ASN cc_start: 0.8656 (t0) cc_final: 0.8360 (t0) REVERT: A 238 GLN cc_start: 0.8950 (mp10) cc_final: 0.8293 (mp10) REVERT: A 266 ILE cc_start: 0.9248 (mt) cc_final: 0.9007 (tp) REVERT: A 316 ASN cc_start: 0.8289 (t0) cc_final: 0.7662 (t0) REVERT: A 333 ILE cc_start: 0.9189 (pt) cc_final: 0.8882 (pt) REVERT: A 337 LEU cc_start: 0.9500 (mt) cc_final: 0.9254 (mt) REVERT: A 344 LEU cc_start: 0.8267 (tt) cc_final: 0.7937 (tt) REVERT: A 370 MET cc_start: 0.6918 (mtm) cc_final: 0.6696 (mmm) REVERT: A 385 TYR cc_start: 0.8004 (t80) cc_final: 0.7783 (t80) REVERT: A 410 TYR cc_start: 0.8160 (t80) cc_final: 0.7935 (t80) REVERT: A 431 LEU cc_start: 0.8968 (tp) cc_final: 0.8728 (tp) REVERT: A 447 ILE cc_start: 0.9593 (mt) cc_final: 0.9383 (mt) REVERT: A 460 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7658 (mtpt) REVERT: A 495 TYR cc_start: 0.8003 (m-10) cc_final: 0.7764 (m-10) REVERT: A 538 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6940 (ttt-90) REVERT: A 567 GLN cc_start: 0.9131 (pm20) cc_final: 0.8829 (pm20) REVERT: A 592 TYR cc_start: 0.8125 (t80) cc_final: 0.6960 (t80) REVERT: H 21 VAL cc_start: 0.8229 (t) cc_final: 0.8008 (t) REVERT: H 22 GLN cc_start: 0.6626 (mp10) cc_final: 0.6344 (mp10) REVERT: H 49 SER cc_start: 0.8373 (p) cc_final: 0.8134 (p) REVERT: H 76 ASP cc_start: 0.8550 (t0) cc_final: 0.8332 (t0) REVERT: H 120 TYR cc_start: 0.7796 (m-80) cc_final: 0.7320 (m-80) REVERT: H 128 ASP cc_start: 0.8469 (t70) cc_final: 0.7709 (t70) REVERT: H 129 TYR cc_start: 0.8802 (m-10) cc_final: 0.8422 (m-10) REVERT: L 60 PHE cc_start: 0.8172 (m-10) cc_final: 0.7699 (m-10) REVERT: L 62 GLN cc_start: 0.6008 (tp40) cc_final: 0.5748 (tp40) REVERT: L 100 HIS cc_start: 0.7236 (m90) cc_final: 0.6700 (m90) REVERT: L 121 THR cc_start: 0.7580 (p) cc_final: 0.7097 (t) REVERT: V 18 GLN cc_start: 0.8521 (mm110) cc_final: 0.7980 (mp10) REVERT: V 20 GLN cc_start: 0.7338 (mm110) cc_final: 0.6984 (mm-40) REVERT: V 37 CYS cc_start: 0.4384 (p) cc_final: 0.3898 (p) REVERT: V 38 LYS cc_start: 0.7804 (tttt) cc_final: 0.7337 (ttmt) REVERT: V 43 THR cc_start: 0.8135 (m) cc_final: 0.7794 (p) REVERT: V 51 TRP cc_start: 0.8437 (m100) cc_final: 0.8109 (m100) REVERT: V 62 TRP cc_start: 0.9104 (t60) cc_final: 0.8539 (t60) REVERT: V 67 ASN cc_start: 0.8041 (t0) cc_final: 0.7646 (t0) REVERT: V 79 PHE cc_start: 0.7124 (m-10) cc_final: 0.6795 (m-10) REVERT: V 92 THR cc_start: 0.8608 (p) cc_final: 0.8180 (t) REVERT: V 105 ASP cc_start: 0.8683 (m-30) cc_final: 0.8279 (m-30) REVERT: V 123 TYR cc_start: 0.7059 (m-10) cc_final: 0.6789 (m-10) REVERT: V 151 ILE cc_start: 0.8302 (mt) cc_final: 0.7963 (mt) REVERT: V 173 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7428 (tppt) REVERT: V 176 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7656 (mm-40) REVERT: V 184 TRP cc_start: 0.9110 (m100) cc_final: 0.8427 (m100) REVERT: V 204 TYR cc_start: 0.8117 (t80) cc_final: 0.7562 (t80) REVERT: V 246 THR cc_start: 0.8768 (p) cc_final: 0.8561 (p) REVERT: V 251 THR cc_start: 0.8255 (m) cc_final: 0.7823 (m) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1676 time to fit residues: 88.8877 Evaluate side-chains 312 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 391 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN V 65 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139807 restraints weight = 15315.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145356 restraints weight = 8866.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149363 restraints weight = 5738.918| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8076 Z= 0.137 Angle : 0.672 12.233 11000 Z= 0.336 Chirality : 0.044 0.336 1215 Planarity : 0.004 0.057 1354 Dihedral : 5.619 41.746 1202 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.91 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 1.08 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.55 (0.27), residues: 978 helix: 0.52 (0.26), residues: 386 sheet: -0.35 (0.37), residues: 182 loop : -1.16 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 220 HIS 0.005 0.001 HIS A 240 PHE 0.027 0.002 PHE A 440 TYR 0.024 0.002 TYR V 48 ARG 0.008 0.001 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 1) link_NAG-ASN : angle 4.03351 ( 3) link_BETA1-4 : bond 0.01347 ( 1) link_BETA1-4 : angle 1.81259 ( 3) hydrogen bonds : bond 0.04317 ( 349) hydrogen bonds : angle 4.98364 ( 954) SS BOND : bond 0.00389 ( 5) SS BOND : angle 0.72892 ( 10) covalent geometry : bond 0.00298 ( 8069) covalent geometry : angle 0.66857 (10984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9123 (p) cc_final: 0.8885 (p) REVERT: A 108 ILE cc_start: 0.8874 (mt) cc_final: 0.8514 (mt) REVERT: A 111 GLN cc_start: 0.9290 (tt0) cc_final: 0.8939 (tm-30) REVERT: A 121 TYR cc_start: 0.9109 (t80) cc_final: 0.8582 (t80) REVERT: A 148 ILE cc_start: 0.8333 (mt) cc_final: 0.8001 (mt) REVERT: A 184 LEU cc_start: 0.9173 (tp) cc_final: 0.8812 (tp) REVERT: A 193 ASP cc_start: 0.8325 (p0) cc_final: 0.8094 (m-30) REVERT: A 195 LEU cc_start: 0.8936 (mt) cc_final: 0.8590 (mt) REVERT: A 205 ASN cc_start: 0.8659 (t0) cc_final: 0.8285 (t0) REVERT: A 222 LEU cc_start: 0.9139 (mm) cc_final: 0.8713 (mm) REVERT: A 238 GLN cc_start: 0.8937 (mp10) cc_final: 0.8251 (mp10) REVERT: A 266 ILE cc_start: 0.9215 (mt) cc_final: 0.8997 (tp) REVERT: A 310 LEU cc_start: 0.8034 (tt) cc_final: 0.7727 (mt) REVERT: A 316 ASN cc_start: 0.8146 (t0) cc_final: 0.7657 (t0) REVERT: A 333 ILE cc_start: 0.9135 (pt) cc_final: 0.8797 (pt) REVERT: A 337 LEU cc_start: 0.9479 (mt) cc_final: 0.9238 (mt) REVERT: A 344 LEU cc_start: 0.8421 (tt) cc_final: 0.7998 (tt) REVERT: A 370 MET cc_start: 0.6599 (mtm) cc_final: 0.6374 (mmm) REVERT: A 385 TYR cc_start: 0.8043 (t80) cc_final: 0.7769 (t80) REVERT: A 410 TYR cc_start: 0.8069 (t80) cc_final: 0.7623 (t80) REVERT: A 422 PHE cc_start: 0.7777 (t80) cc_final: 0.7548 (t80) REVERT: A 426 ILE cc_start: 0.9183 (mt) cc_final: 0.8846 (mt) REVERT: A 447 ILE cc_start: 0.9576 (mt) cc_final: 0.9343 (mt) REVERT: A 453 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 460 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7696 (mtpt) REVERT: A 495 TYR cc_start: 0.8070 (m-10) cc_final: 0.7716 (m-10) REVERT: A 538 ARG cc_start: 0.7388 (mtm180) cc_final: 0.6884 (ttt-90) REVERT: A 567 GLN cc_start: 0.9126 (pm20) cc_final: 0.8807 (pm20) REVERT: H 22 GLN cc_start: 0.6434 (mp10) cc_final: 0.6162 (mp10) REVERT: H 49 SER cc_start: 0.8524 (p) cc_final: 0.8260 (p) REVERT: H 76 ASP cc_start: 0.8826 (t0) cc_final: 0.8269 (t0) REVERT: H 84 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8239 (tppt) REVERT: H 120 TYR cc_start: 0.7938 (m-80) cc_final: 0.7511 (m-80) REVERT: L 60 PHE cc_start: 0.8157 (m-10) cc_final: 0.7710 (m-10) REVERT: L 77 ASN cc_start: 0.8859 (t0) cc_final: 0.8651 (t0) REVERT: L 100 HIS cc_start: 0.7321 (m90) cc_final: 0.6785 (m90) REVERT: L 114 GLN cc_start: 0.7774 (pm20) cc_final: 0.7254 (pm20) REVERT: L 122 PHE cc_start: 0.7622 (m-10) cc_final: 0.7419 (m-10) REVERT: V 18 GLN cc_start: 0.8538 (mm110) cc_final: 0.8198 (mm110) REVERT: V 20 GLN cc_start: 0.7399 (mm110) cc_final: 0.7019 (mm-40) REVERT: V 37 CYS cc_start: 0.4511 (p) cc_final: 0.4050 (p) REVERT: V 38 LYS cc_start: 0.7798 (tttt) cc_final: 0.7265 (mttt) REVERT: V 43 THR cc_start: 0.8182 (m) cc_final: 0.7841 (p) REVERT: V 51 TRP cc_start: 0.8445 (m100) cc_final: 0.8070 (m100) REVERT: V 62 TRP cc_start: 0.9033 (t60) cc_final: 0.8393 (t60) REVERT: V 67 ASN cc_start: 0.8121 (t0) cc_final: 0.7684 (t0) REVERT: V 79 PHE cc_start: 0.6959 (m-10) cc_final: 0.6678 (m-10) REVERT: V 92 THR cc_start: 0.8608 (p) cc_final: 0.8192 (t) REVERT: V 105 ASP cc_start: 0.8553 (m-30) cc_final: 0.8141 (m-30) REVERT: V 151 ILE cc_start: 0.8489 (mt) cc_final: 0.8176 (mt) REVERT: V 173 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7522 (tppt) REVERT: V 176 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7649 (mm-40) REVERT: V 184 TRP cc_start: 0.9074 (m100) cc_final: 0.8572 (m100) REVERT: V 204 TYR cc_start: 0.8216 (t80) cc_final: 0.7812 (t80) REVERT: V 251 THR cc_start: 0.8201 (m) cc_final: 0.7816 (m) outliers start: 1 outliers final: 1 residues processed: 365 average time/residue: 0.1743 time to fit residues: 88.5408 Evaluate side-chains 317 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 391 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN V 65 ASN V 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139772 restraints weight = 15644.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145268 restraints weight = 9051.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149278 restraints weight = 5860.998| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8076 Z= 0.131 Angle : 0.669 11.864 11000 Z= 0.335 Chirality : 0.044 0.346 1215 Planarity : 0.004 0.052 1354 Dihedral : 5.510 40.779 1202 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.47 (0.27), residues: 978 helix: 0.53 (0.26), residues: 386 sheet: -0.33 (0.37), residues: 181 loop : -1.04 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 220 HIS 0.005 0.002 HIS A 143 PHE 0.027 0.002 PHE A 440 TYR 0.017 0.002 TYR A 171 ARG 0.003 0.000 ARG H 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 3.76856 ( 3) link_BETA1-4 : bond 0.00826 ( 1) link_BETA1-4 : angle 1.62996 ( 3) hydrogen bonds : bond 0.04244 ( 349) hydrogen bonds : angle 4.92953 ( 954) SS BOND : bond 0.00397 ( 5) SS BOND : angle 0.80916 ( 10) covalent geometry : bond 0.00293 ( 8069) covalent geometry : angle 0.66511 (10984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9122 (p) cc_final: 0.8818 (t) REVERT: A 108 ILE cc_start: 0.8960 (mt) cc_final: 0.8500 (mt) REVERT: A 111 GLN cc_start: 0.9266 (tt0) cc_final: 0.8940 (tm-30) REVERT: A 121 TYR cc_start: 0.9076 (t80) cc_final: 0.8498 (t80) REVERT: A 124 MET cc_start: 0.8700 (mmp) cc_final: 0.8492 (mmp) REVERT: A 184 LEU cc_start: 0.9178 (tp) cc_final: 0.8817 (tp) REVERT: A 193 ASP cc_start: 0.8343 (p0) cc_final: 0.8099 (m-30) REVERT: A 205 ASN cc_start: 0.8671 (t0) cc_final: 0.8232 (t0) REVERT: A 238 GLN cc_start: 0.8930 (mp10) cc_final: 0.8250 (mp10) REVERT: A 246 GLN cc_start: 0.7589 (pm20) cc_final: 0.7297 (tt0) REVERT: A 266 ILE cc_start: 0.9213 (mt) cc_final: 0.8974 (tp) REVERT: A 316 ASN cc_start: 0.8129 (t0) cc_final: 0.7650 (t0) REVERT: A 333 ILE cc_start: 0.9144 (pt) cc_final: 0.8797 (pt) REVERT: A 337 LEU cc_start: 0.9474 (mt) cc_final: 0.9225 (mt) REVERT: A 344 LEU cc_start: 0.8403 (tt) cc_final: 0.7935 (tt) REVERT: A 385 TYR cc_start: 0.8089 (t80) cc_final: 0.7797 (t80) REVERT: A 410 TYR cc_start: 0.8088 (t80) cc_final: 0.7785 (t80) REVERT: A 426 ILE cc_start: 0.9199 (mt) cc_final: 0.8907 (mt) REVERT: A 447 ILE cc_start: 0.9576 (mt) cc_final: 0.9350 (mt) REVERT: A 460 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7725 (mtpt) REVERT: A 495 TYR cc_start: 0.8025 (m-10) cc_final: 0.7719 (m-10) REVERT: A 538 ARG cc_start: 0.7427 (mtm180) cc_final: 0.6865 (ttt-90) REVERT: A 567 GLN cc_start: 0.9123 (pm20) cc_final: 0.8795 (pm20) REVERT: A 573 TRP cc_start: 0.8249 (p-90) cc_final: 0.8017 (p-90) REVERT: A 584 SER cc_start: 0.8486 (t) cc_final: 0.8279 (p) REVERT: A 592 TYR cc_start: 0.8323 (t80) cc_final: 0.7790 (t80) REVERT: H 22 GLN cc_start: 0.6481 (mp10) cc_final: 0.6194 (mp10) REVERT: H 49 SER cc_start: 0.8831 (p) cc_final: 0.8536 (p) REVERT: H 120 TYR cc_start: 0.7834 (m-80) cc_final: 0.7373 (m-80) REVERT: L 60 PHE cc_start: 0.7962 (m-10) cc_final: 0.7623 (m-10) REVERT: L 62 GLN cc_start: 0.5952 (tp40) cc_final: 0.4969 (tm-30) REVERT: L 71 LEU cc_start: 0.9014 (mt) cc_final: 0.8609 (mt) REVERT: L 77 ASN cc_start: 0.8885 (t0) cc_final: 0.8665 (t0) REVERT: L 100 HIS cc_start: 0.7350 (m90) cc_final: 0.6819 (m90) REVERT: L 114 GLN cc_start: 0.7815 (pm20) cc_final: 0.7188 (pm20) REVERT: L 122 PHE cc_start: 0.7650 (m-10) cc_final: 0.7439 (m-10) REVERT: V 18 GLN cc_start: 0.8520 (mm110) cc_final: 0.8180 (mm110) REVERT: V 20 GLN cc_start: 0.7469 (mm110) cc_final: 0.7044 (mm-40) REVERT: V 37 CYS cc_start: 0.4349 (p) cc_final: 0.3981 (p) REVERT: V 38 LYS cc_start: 0.7822 (tttt) cc_final: 0.7299 (ttmt) REVERT: V 43 THR cc_start: 0.8095 (m) cc_final: 0.7370 (p) REVERT: V 51 TRP cc_start: 0.8496 (m100) cc_final: 0.7967 (m100) REVERT: V 62 TRP cc_start: 0.9058 (t60) cc_final: 0.8467 (t60) REVERT: V 67 ASN cc_start: 0.8164 (t0) cc_final: 0.7738 (t0) REVERT: V 79 PHE cc_start: 0.7110 (m-10) cc_final: 0.6604 (m-10) REVERT: V 92 THR cc_start: 0.8608 (p) cc_final: 0.8185 (t) REVERT: V 105 ASP cc_start: 0.8457 (m-30) cc_final: 0.8076 (m-30) REVERT: V 151 ILE cc_start: 0.8508 (mt) cc_final: 0.8125 (mt) REVERT: V 173 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7490 (tppt) REVERT: V 176 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7703 (mm-40) REVERT: V 184 TRP cc_start: 0.9051 (m100) cc_final: 0.8537 (m100) REVERT: V 238 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7380 (tp-100) REVERT: V 251 THR cc_start: 0.8251 (m) cc_final: 0.7861 (m) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1726 time to fit residues: 87.0736 Evaluate side-chains 308 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 368 ASN A 391 ASN A 456 HIS ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140894 restraints weight = 15472.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146504 restraints weight = 8872.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150574 restraints weight = 5699.015| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8076 Z= 0.133 Angle : 0.668 11.936 11000 Z= 0.332 Chirality : 0.044 0.356 1215 Planarity : 0.004 0.049 1354 Dihedral : 5.446 40.530 1202 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.41 (0.27), residues: 978 helix: 0.58 (0.26), residues: 388 sheet: -0.30 (0.38), residues: 182 loop : -1.01 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 220 HIS 0.005 0.001 HIS A 143 PHE 0.022 0.002 PHE A 440 TYR 0.022 0.002 TYR V 48 ARG 0.004 0.000 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 1) link_NAG-ASN : angle 3.32481 ( 3) link_BETA1-4 : bond 0.01238 ( 1) link_BETA1-4 : angle 1.83938 ( 3) hydrogen bonds : bond 0.04194 ( 349) hydrogen bonds : angle 4.92114 ( 954) SS BOND : bond 0.00494 ( 5) SS BOND : angle 0.98481 ( 10) covalent geometry : bond 0.00302 ( 8069) covalent geometry : angle 0.66534 (10984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9109 (p) cc_final: 0.8850 (p) REVERT: A 108 ILE cc_start: 0.8919 (mt) cc_final: 0.8496 (mt) REVERT: A 111 GLN cc_start: 0.9208 (tt0) cc_final: 0.8936 (tm-30) REVERT: A 119 LEU cc_start: 0.8634 (tt) cc_final: 0.8237 (tp) REVERT: A 121 TYR cc_start: 0.8987 (t80) cc_final: 0.8375 (t80) REVERT: A 124 MET cc_start: 0.8711 (mmp) cc_final: 0.8480 (mmp) REVERT: A 147 CYS cc_start: 0.8807 (t) cc_final: 0.8549 (t) REVERT: A 184 LEU cc_start: 0.9176 (tp) cc_final: 0.8811 (tp) REVERT: A 195 LEU cc_start: 0.9263 (mt) cc_final: 0.8924 (mt) REVERT: A 205 ASN cc_start: 0.8601 (t0) cc_final: 0.8114 (t0) REVERT: A 238 GLN cc_start: 0.8914 (mp10) cc_final: 0.8218 (mp10) REVERT: A 246 GLN cc_start: 0.7623 (pm20) cc_final: 0.7345 (tt0) REVERT: A 316 ASN cc_start: 0.8292 (t0) cc_final: 0.7832 (t0) REVERT: A 333 ILE cc_start: 0.9121 (pt) cc_final: 0.8751 (pt) REVERT: A 337 LEU cc_start: 0.9462 (mt) cc_final: 0.9210 (mt) REVERT: A 385 TYR cc_start: 0.8271 (t80) cc_final: 0.8055 (t80) REVERT: A 410 TYR cc_start: 0.8104 (t80) cc_final: 0.7701 (t80) REVERT: A 447 ILE cc_start: 0.9577 (mt) cc_final: 0.9342 (mt) REVERT: A 460 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7724 (mtpt) REVERT: A 495 TYR cc_start: 0.8014 (m-10) cc_final: 0.7726 (m-10) REVERT: A 538 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6775 (ttt-90) REVERT: A 567 GLN cc_start: 0.9113 (pm20) cc_final: 0.8775 (pm20) REVERT: A 573 TRP cc_start: 0.8282 (p-90) cc_final: 0.7897 (p-90) REVERT: A 592 TYR cc_start: 0.8320 (t80) cc_final: 0.7927 (t80) REVERT: H 22 GLN cc_start: 0.6461 (mp10) cc_final: 0.6127 (mp10) REVERT: H 49 SER cc_start: 0.8888 (p) cc_final: 0.8641 (p) REVERT: H 50 TYR cc_start: 0.8043 (m-80) cc_final: 0.7087 (m-80) REVERT: H 76 ASP cc_start: 0.8699 (t0) cc_final: 0.8470 (t0) REVERT: H 84 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8277 (tppt) REVERT: H 120 TYR cc_start: 0.7871 (m-80) cc_final: 0.7410 (m-80) REVERT: L 60 PHE cc_start: 0.7983 (m-10) cc_final: 0.7719 (m-10) REVERT: L 62 GLN cc_start: 0.5918 (tp40) cc_final: 0.4938 (tm-30) REVERT: L 77 ASN cc_start: 0.8870 (t0) cc_final: 0.8637 (t0) REVERT: L 83 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8571 (Cg_endo) REVERT: L 86 PHE cc_start: 0.8702 (m-80) cc_final: 0.8500 (m-80) REVERT: L 100 HIS cc_start: 0.7359 (m90) cc_final: 0.6816 (m90) REVERT: L 114 GLN cc_start: 0.7837 (pm20) cc_final: 0.7168 (pm20) REVERT: L 121 THR cc_start: 0.7231 (p) cc_final: 0.6874 (p) REVERT: V 18 GLN cc_start: 0.8517 (mm110) cc_final: 0.8162 (mm110) REVERT: V 20 GLN cc_start: 0.7535 (mm110) cc_final: 0.7095 (mm-40) REVERT: V 38 LYS cc_start: 0.7866 (tttt) cc_final: 0.7371 (ttmt) REVERT: V 43 THR cc_start: 0.7889 (m) cc_final: 0.7467 (p) REVERT: V 51 TRP cc_start: 0.8338 (m100) cc_final: 0.7790 (m100) REVERT: V 62 TRP cc_start: 0.8974 (t60) cc_final: 0.8482 (t60) REVERT: V 67 ASN cc_start: 0.8258 (t0) cc_final: 0.7928 (t0) REVERT: V 92 THR cc_start: 0.8578 (p) cc_final: 0.8159 (t) REVERT: V 105 ASP cc_start: 0.8470 (m-30) cc_final: 0.8076 (m-30) REVERT: V 151 ILE cc_start: 0.8440 (mt) cc_final: 0.8091 (mt) REVERT: V 173 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7365 (tppt) REVERT: V 176 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7739 (mm-40) REVERT: V 184 TRP cc_start: 0.9009 (m100) cc_final: 0.8512 (m100) REVERT: V 238 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7629 (tp-100) REVERT: V 239 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7872 (tm-30) REVERT: V 251 THR cc_start: 0.8315 (m) cc_final: 0.7926 (m) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1674 time to fit residues: 80.6201 Evaluate side-chains 298 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 368 ASN A 391 ASN H 58 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN V 187 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138694 restraints weight = 15660.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144268 restraints weight = 8963.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.148275 restraints weight = 5751.642| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8076 Z= 0.144 Angle : 0.671 11.776 11000 Z= 0.337 Chirality : 0.044 0.361 1215 Planarity : 0.004 0.049 1354 Dihedral : 5.466 38.908 1202 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.47 (0.27), residues: 978 helix: 0.51 (0.26), residues: 386 sheet: -0.24 (0.38), residues: 176 loop : -1.04 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 220 HIS 0.006 0.001 HIS A 223 PHE 0.023 0.002 PHE A 440 TYR 0.017 0.002 TYR A 171 ARG 0.006 0.001 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 1) link_NAG-ASN : angle 3.26434 ( 3) link_BETA1-4 : bond 0.01170 ( 1) link_BETA1-4 : angle 1.79226 ( 3) hydrogen bonds : bond 0.04271 ( 349) hydrogen bonds : angle 4.92022 ( 954) SS BOND : bond 0.00458 ( 5) SS BOND : angle 0.83189 ( 10) covalent geometry : bond 0.00323 ( 8069) covalent geometry : angle 0.66799 (10984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9064 (p) cc_final: 0.8789 (p) REVERT: A 108 ILE cc_start: 0.8935 (mt) cc_final: 0.8524 (mt) REVERT: A 111 GLN cc_start: 0.9172 (tt0) cc_final: 0.8933 (tm-30) REVERT: A 121 TYR cc_start: 0.9007 (t80) cc_final: 0.8372 (t80) REVERT: A 124 MET cc_start: 0.8739 (mmp) cc_final: 0.8444 (mmp) REVERT: A 184 LEU cc_start: 0.9203 (tp) cc_final: 0.8844 (tp) REVERT: A 205 ASN cc_start: 0.8779 (t0) cc_final: 0.8261 (t0) REVERT: A 238 GLN cc_start: 0.8619 (mp10) cc_final: 0.8125 (mp10) REVERT: A 246 GLN cc_start: 0.7620 (pm20) cc_final: 0.7337 (tt0) REVERT: A 266 ILE cc_start: 0.9220 (mt) cc_final: 0.8984 (tp) REVERT: A 295 LEU cc_start: 0.8110 (tp) cc_final: 0.7842 (tt) REVERT: A 316 ASN cc_start: 0.8340 (t0) cc_final: 0.7872 (t0) REVERT: A 333 ILE cc_start: 0.9136 (pt) cc_final: 0.8765 (pt) REVERT: A 337 LEU cc_start: 0.9474 (mt) cc_final: 0.9214 (mt) REVERT: A 344 LEU cc_start: 0.8444 (tt) cc_final: 0.7836 (tt) REVERT: A 385 TYR cc_start: 0.8274 (t80) cc_final: 0.8061 (t80) REVERT: A 447 ILE cc_start: 0.9599 (mt) cc_final: 0.9359 (mt) REVERT: A 460 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7757 (mtpt) REVERT: A 495 TYR cc_start: 0.8047 (m-10) cc_final: 0.7768 (m-10) REVERT: A 538 ARG cc_start: 0.7373 (mtm180) cc_final: 0.6723 (ttt-90) REVERT: A 567 GLN cc_start: 0.9122 (pm20) cc_final: 0.8772 (pm20) REVERT: A 573 TRP cc_start: 0.8378 (p-90) cc_final: 0.7982 (p-90) REVERT: A 592 TYR cc_start: 0.8285 (t80) cc_final: 0.7960 (t80) REVERT: H 50 TYR cc_start: 0.8177 (m-80) cc_final: 0.7808 (m-80) REVERT: H 84 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8191 (tppt) REVERT: H 86 LYS cc_start: 0.8481 (ptpp) cc_final: 0.7391 (mmtt) REVERT: H 120 TYR cc_start: 0.7916 (m-80) cc_final: 0.7443 (m-80) REVERT: L 60 PHE cc_start: 0.7974 (m-10) cc_final: 0.7750 (m-10) REVERT: L 71 LEU cc_start: 0.8973 (mt) cc_final: 0.8579 (mt) REVERT: L 77 ASN cc_start: 0.8908 (t0) cc_final: 0.8656 (t0) REVERT: L 83 PRO cc_start: 0.8845 (Cg_exo) cc_final: 0.8591 (Cg_endo) REVERT: L 86 PHE cc_start: 0.8742 (m-80) cc_final: 0.8461 (m-80) REVERT: L 100 HIS cc_start: 0.7387 (m90) cc_final: 0.6858 (m90) REVERT: V 18 GLN cc_start: 0.8561 (mm110) cc_final: 0.8208 (mm110) REVERT: V 20 GLN cc_start: 0.7592 (mm110) cc_final: 0.7148 (mm-40) REVERT: V 38 LYS cc_start: 0.7851 (tttt) cc_final: 0.7349 (ttmt) REVERT: V 43 THR cc_start: 0.7994 (m) cc_final: 0.7187 (p) REVERT: V 51 TRP cc_start: 0.8383 (m100) cc_final: 0.7601 (m100) REVERT: V 67 ASN cc_start: 0.8327 (t0) cc_final: 0.7969 (t0) REVERT: V 92 THR cc_start: 0.8644 (p) cc_final: 0.8244 (t) REVERT: V 105 ASP cc_start: 0.8470 (m-30) cc_final: 0.8006 (m-30) REVERT: V 151 ILE cc_start: 0.8473 (mt) cc_final: 0.8148 (mt) REVERT: V 173 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7469 (tppt) REVERT: V 176 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7741 (mm-40) REVERT: V 184 TRP cc_start: 0.9059 (m100) cc_final: 0.8565 (m100) REVERT: V 236 TYR cc_start: 0.8670 (m-80) cc_final: 0.7649 (m-10) REVERT: V 239 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7855 (tm-30) REVERT: V 251 THR cc_start: 0.8175 (m) cc_final: 0.7787 (m) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1700 time to fit residues: 81.2618 Evaluate side-chains 298 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 368 ASN A 391 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN V 238 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133874 restraints weight = 15576.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139230 restraints weight = 9014.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143134 restraints weight = 5832.098| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.7224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8076 Z= 0.175 Angle : 0.712 11.798 11000 Z= 0.361 Chirality : 0.045 0.273 1215 Planarity : 0.005 0.051 1354 Dihedral : 5.627 44.324 1202 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.52 (0.27), residues: 978 helix: 0.41 (0.26), residues: 384 sheet: -0.20 (0.37), residues: 189 loop : -1.06 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 130 HIS 0.008 0.001 HIS A 143 PHE 0.021 0.002 PHE A 440 TYR 0.016 0.002 TYR A 289 ARG 0.007 0.001 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 1) link_NAG-ASN : angle 3.29026 ( 3) link_BETA1-4 : bond 0.01432 ( 1) link_BETA1-4 : angle 1.99529 ( 3) hydrogen bonds : bond 0.04478 ( 349) hydrogen bonds : angle 4.90060 ( 954) SS BOND : bond 0.00354 ( 5) SS BOND : angle 0.98388 ( 10) covalent geometry : bond 0.00391 ( 8069) covalent geometry : angle 0.70873 (10984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 THR cc_start: 0.9030 (p) cc_final: 0.8793 (p) REVERT: A 108 ILE cc_start: 0.8963 (mt) cc_final: 0.8524 (mt) REVERT: A 121 TYR cc_start: 0.9030 (t80) cc_final: 0.8475 (t80) REVERT: A 184 LEU cc_start: 0.9239 (tp) cc_final: 0.8886 (tp) REVERT: A 238 GLN cc_start: 0.8600 (mp10) cc_final: 0.8035 (mt0) REVERT: A 246 GLN cc_start: 0.7622 (pm20) cc_final: 0.7374 (tt0) REVERT: A 266 ILE cc_start: 0.9234 (mt) cc_final: 0.8999 (tp) REVERT: A 316 ASN cc_start: 0.8441 (t0) cc_final: 0.7999 (t0) REVERT: A 328 ASP cc_start: 0.8169 (m-30) cc_final: 0.7892 (m-30) REVERT: A 333 ILE cc_start: 0.9133 (pt) cc_final: 0.8764 (pt) REVERT: A 337 LEU cc_start: 0.9470 (mt) cc_final: 0.9184 (mt) REVERT: A 385 TYR cc_start: 0.8563 (t80) cc_final: 0.8283 (t80) REVERT: A 393 ASP cc_start: 0.8647 (t0) cc_final: 0.8255 (t70) REVERT: A 447 ILE cc_start: 0.9596 (mt) cc_final: 0.9365 (mt) REVERT: A 453 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 460 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7852 (mtpt) REVERT: A 538 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6781 (ttt-90) REVERT: A 567 GLN cc_start: 0.9151 (pm20) cc_final: 0.8779 (pm20) REVERT: A 573 TRP cc_start: 0.8443 (p-90) cc_final: 0.8035 (p-90) REVERT: A 592 TYR cc_start: 0.8297 (t80) cc_final: 0.8084 (t80) REVERT: H 49 SER cc_start: 0.8844 (p) cc_final: 0.8633 (p) REVERT: H 50 TYR cc_start: 0.8210 (m-80) cc_final: 0.7911 (m-80) REVERT: H 84 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8216 (tppt) REVERT: H 86 LYS cc_start: 0.8597 (ptpp) cc_final: 0.7463 (mmtt) REVERT: L 37 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7534 (tp-100) REVERT: L 77 ASN cc_start: 0.8927 (t0) cc_final: 0.8666 (t0) REVERT: L 86 PHE cc_start: 0.8817 (m-80) cc_final: 0.8485 (m-80) REVERT: L 100 HIS cc_start: 0.7451 (m90) cc_final: 0.6946 (m90) REVERT: V 18 GLN cc_start: 0.8581 (mm110) cc_final: 0.8247 (mp10) REVERT: V 38 LYS cc_start: 0.7863 (tttt) cc_final: 0.7392 (ttmt) REVERT: V 43 THR cc_start: 0.7857 (m) cc_final: 0.7283 (m) REVERT: V 51 TRP cc_start: 0.7719 (m100) cc_final: 0.7513 (m100) REVERT: V 67 ASN cc_start: 0.8416 (t0) cc_final: 0.8095 (t0) REVERT: V 92 THR cc_start: 0.8649 (p) cc_final: 0.8232 (t) REVERT: V 102 THR cc_start: 0.6551 (p) cc_final: 0.5960 (p) REVERT: V 105 ASP cc_start: 0.8447 (m-30) cc_final: 0.7975 (m-30) REVERT: V 151 ILE cc_start: 0.8341 (mt) cc_final: 0.7949 (mt) REVERT: V 173 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7552 (tppt) REVERT: V 176 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7916 (mm-40) REVERT: V 184 TRP cc_start: 0.9043 (m100) cc_final: 0.8488 (m100) REVERT: V 236 TYR cc_start: 0.8743 (m-80) cc_final: 0.7826 (m-10) REVERT: V 239 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7858 (tm-30) REVERT: V 241 TYR cc_start: 0.8652 (t80) cc_final: 0.7800 (t80) REVERT: V 251 THR cc_start: 0.8195 (m) cc_final: 0.7807 (m) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1691 time to fit residues: 79.9936 Evaluate side-chains 303 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.0000 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 368 ASN A 391 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN V 65 ASN V 238 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.159578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136826 restraints weight = 15626.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142172 restraints weight = 9011.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146078 restraints weight = 5807.033| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8076 Z= 0.147 Angle : 0.686 11.788 11000 Z= 0.350 Chirality : 0.045 0.319 1215 Planarity : 0.004 0.048 1354 Dihedral : 5.668 48.585 1202 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.56 (0.27), residues: 978 helix: 0.41 (0.25), residues: 387 sheet: -0.27 (0.38), residues: 183 loop : -1.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 62 HIS 0.007 0.001 HIS A 143 PHE 0.027 0.002 PHE A 440 TYR 0.020 0.002 TYR A 312 ARG 0.007 0.001 ARG V 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 2.85628 ( 3) link_BETA1-4 : bond 0.01314 ( 1) link_BETA1-4 : angle 1.72445 ( 3) hydrogen bonds : bond 0.04321 ( 349) hydrogen bonds : angle 4.94189 ( 954) SS BOND : bond 0.00342 ( 5) SS BOND : angle 1.02110 ( 10) covalent geometry : bond 0.00330 ( 8069) covalent geometry : angle 0.68392 (10984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3338.27 seconds wall clock time: 59 minutes 30.54 seconds (3570.54 seconds total)