Starting phenix.real_space_refine on Thu Aug 6 19:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2026/8t4m_41036.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 C 10984 2.51 5 N 2864 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17000 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 5, 'GLN:plan1': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: C, B, A Time building chain proxies: 3.72, per 1000 atoms: 0.22 Number of scatterers: 17000 At special positions: 0 Unit cell: (112.288, 112.288, 128.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 4 15.00 O 3008 8.00 N 2864 7.00 C 10984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 612.4 milliseconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 73.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 289 Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP D 589 " --> pdb=" O THR D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 620 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 289 Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 289 Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 289 Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER D 204 " --> pdb=" O ASN D 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR D 524 " --> pdb=" O LYS D 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 528 " --> pdb=" O THR D 524 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR C 524 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 524 " --> pdb=" O LYS B 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A 524 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3363 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: 3.26 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5404 1.35 - 1.47: 4290 1.47 - 1.58: 7450 1.58 - 1.70: 8 1.70 - 1.82: 244 Bond restraints: 17396 Sorted by residual: bond pdb=" C4' CMP D 901 " pdb=" C5' CMP D 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C4' CMP A 901 " pdb=" C5' CMP A 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C4' CMP C 901 " pdb=" C5' CMP C 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C4' CMP B 901 " pdb=" C5' CMP B 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" CA PRO D 577 " pdb=" C PRO D 577 " ideal model delta sigma weight residual 1.520 1.537 -0.018 1.42e-02 4.96e+03 1.52e+00 ... (remaining 17391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 23312 2.29 - 4.58: 180 4.58 - 6.87: 40 6.87 - 9.16: 20 9.16 - 11.45: 8 Bond angle restraints: 23560 Sorted by residual: angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CB MET A 215 " pdb=" CG MET A 215 " pdb=" SD MET A 215 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 23555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 9008 15.74 - 31.48: 1052 31.48 - 47.22: 212 47.22 - 62.96: 80 62.96 - 78.70: 8 Dihedral angle restraints: 10360 sinusoidal: 4084 harmonic: 6276 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PRO C 210 " pdb=" CA PRO C 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP B 209 " pdb=" C ASP B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N PRO A 210 " pdb=" CA PRO A 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 10357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2232 0.053 - 0.107: 360 0.107 - 0.160: 32 0.160 - 0.213: 0 0.213 - 0.266: 4 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C2' CMP B 901 " pdb=" C1' CMP B 901 " pdb=" C3' CMP B 901 " pdb=" O2' CMP B 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' CMP A 901 " pdb=" C1' CMP A 901 " pdb=" C3' CMP A 901 " pdb=" O2' CMP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' CMP C 901 " pdb=" C1' CMP C 901 " pdb=" C3' CMP C 901 " pdb=" O2' CMP C 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2625 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO C 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO D 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO B 481 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " 0.024 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2200 2.75 - 3.29: 16867 3.29 - 3.83: 28535 3.83 - 4.36: 31712 4.36 - 4.90: 57736 Nonbonded interactions: 137050 Sorted by model distance: nonbonded pdb=" NZ LYS D 108 " pdb=" OE2 GLU C 436 " model vdw 2.217 3.120 nonbonded pdb=" OE2 GLU D 436 " pdb=" NZ LYS A 108 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS B 108 " pdb=" OE2 GLU A 436 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS C 108 " pdb=" OE2 GLU B 436 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR D 435 " pdb=" OE1 GLU A 452 " model vdw 2.240 3.040 ... (remaining 137045 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.980 Find NCS groups from input model: 0.150 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.002 0.031 17396 Z= 0.112 Angle : 0.606 11.451 23560 Z= 0.287 Chirality : 0.038 0.266 2628 Planarity : 0.003 0.044 2956 Dihedral : 14.520 78.700 6296 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2116 helix: 1.42 (0.13), residues: 1488 sheet: -0.12 (0.55), residues: 88 loop : -1.55 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 467 TYR 0.014 0.001 TYR D 576 PHE 0.005 0.001 PHE A 483 TRP 0.025 0.002 TRP B 133 HIS 0.002 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (17396) covalent geometry : angle 0.60633 / 0.29 (23560) hydrogen bonds : bond 0.09890 / 6.36 ( 1149) hydrogen bonds : angle 4.35095 / 3.30 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: D 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7723 (m-80) REVERT: D 454 ASN cc_start: 0.8443 (p0) cc_final: 0.8179 (p0) REVERT: C 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: C 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7724 (m-80) REVERT: C 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: B 118 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7530 (ptmm) REVERT: B 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: B 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: A 118 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7532 (ptmm) REVERT: A 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: A 454 ASN cc_start: 0.8445 (p0) cc_final: 0.8179 (p0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1187 time to fit residues: 51.0020 Evaluate side-chains 256 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 421 HIS C 421 HIS B 421 HIS A 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123995 restraints weight = 20134.614| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.26 r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17396 Z= 0.146 Angle : 0.558 8.709 23560 Z= 0.267 Chirality : 0.040 0.173 2628 Planarity : 0.004 0.033 2956 Dihedral : 3.882 35.649 2372 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.36 % Allowed : 13.38 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 2116 helix: 1.80 (0.14), residues: 1496 sheet: -0.12 (0.54), residues: 88 loop : -1.39 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.012 0.001 TYR B 411 PHE 0.009 0.001 PHE A 514 TRP 0.017 0.002 TRP A 281 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17396) covalent geometry : angle 0.55774 / 0.27 (23560) hydrogen bonds : bond 0.03309 / 2.20 ( 1149) hydrogen bonds : angle 3.66640 / 2.76 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.558 Fit side-chains REVERT: D 259 PHE cc_start: 0.7933 (m-80) cc_final: 0.7692 (m-80) REVERT: D 286 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: D 287 MET cc_start: 0.7397 (tpp) cc_final: 0.7193 (tpp) REVERT: D 524 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8067 (p) REVERT: D 581 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7945 (tpp80) REVERT: C 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7690 (m-80) REVERT: C 286 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7487 (t-90) REVERT: C 287 MET cc_start: 0.7393 (tpp) cc_final: 0.7188 (tpp) REVERT: C 524 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8066 (p) REVERT: C 581 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7947 (tpp80) REVERT: B 259 PHE cc_start: 0.7936 (m-80) cc_final: 0.7698 (m-80) REVERT: B 286 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7489 (t-90) REVERT: B 287 MET cc_start: 0.7390 (tpp) cc_final: 0.7189 (tpp) REVERT: B 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 581 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7951 (tpp80) REVERT: A 259 PHE cc_start: 0.7943 (m-80) cc_final: 0.7705 (m-80) REVERT: A 286 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7488 (t-90) REVERT: A 287 MET cc_start: 0.7403 (tpp) cc_final: 0.7201 (tpp) REVERT: A 524 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 581 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7956 (tpp80) outliers start: 24 outliers final: 4 residues processed: 268 average time/residue: 0.1086 time to fit residues: 45.9173 Evaluate side-chains 252 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 124 GLN B 124 GLN A 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.166568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118575 restraints weight = 20624.252| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.20 r_work: 0.3268 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 17396 Z= 0.275 Angle : 0.638 9.027 23560 Z= 0.316 Chirality : 0.044 0.178 2628 Planarity : 0.004 0.049 2956 Dihedral : 4.127 38.483 2372 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.21 % Allowed : 13.21 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 2116 helix: 1.63 (0.13), residues: 1496 sheet: 0.03 (0.54), residues: 88 loop : -1.58 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.017 0.002 TYR C 411 PHE 0.010 0.002 PHE B 514 TRP 0.021 0.002 TRP A 281 HIS 0.005 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.27 (17396) covalent geometry : angle 0.63776 / 0.32 (23560) hydrogen bonds : bond 0.04095 / 2.72 ( 1149) hydrogen bonds : angle 3.85733 / 2.89 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.634 Fit side-chains REVERT: D 112 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7706 (ttt-90) REVERT: D 259 PHE cc_start: 0.7871 (m-80) cc_final: 0.7394 (m-80) REVERT: D 287 MET cc_start: 0.7445 (tpp) cc_final: 0.6851 (tpp) REVERT: D 524 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8380 (t) REVERT: D 581 ARG cc_start: 0.8521 (ttp80) cc_final: 0.7968 (tpp80) REVERT: C 112 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7699 (ttt-90) REVERT: C 259 PHE cc_start: 0.7869 (m-80) cc_final: 0.7392 (m-80) REVERT: C 287 MET cc_start: 0.7447 (tpp) cc_final: 0.6851 (tpp) REVERT: C 524 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 581 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7958 (tpp80) REVERT: B 112 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7697 (ttt-90) REVERT: B 259 PHE cc_start: 0.7878 (m-80) cc_final: 0.7400 (m-80) REVERT: B 287 MET cc_start: 0.7447 (tpp) cc_final: 0.6849 (tpp) REVERT: B 524 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8379 (t) REVERT: B 581 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7969 (tpp80) REVERT: A 259 PHE cc_start: 0.7883 (m-80) cc_final: 0.7407 (m-80) REVERT: A 287 MET cc_start: 0.7452 (tpp) cc_final: 0.7065 (tpp) REVERT: A 524 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (t) REVERT: A 581 ARG cc_start: 0.8516 (ttp80) cc_final: 0.7967 (tpp80) outliers start: 39 outliers final: 19 residues processed: 264 average time/residue: 0.1144 time to fit residues: 47.5903 Evaluate side-chains 239 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 208 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128145 restraints weight = 20445.387| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.14 r_work: 0.3439 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17396 Z= 0.112 Angle : 0.533 8.754 23560 Z= 0.255 Chirality : 0.039 0.181 2628 Planarity : 0.003 0.041 2956 Dihedral : 3.922 35.878 2372 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 14.74 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2116 helix: 1.98 (0.14), residues: 1488 sheet: -0.16 (0.54), residues: 88 loop : -1.51 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 467 TYR 0.014 0.001 TYR D 411 PHE 0.010 0.001 PHE A 514 TRP 0.017 0.002 TRP D 133 HIS 0.002 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17396) covalent geometry : angle 0.53305 / 0.26 (23560) hydrogen bonds : bond 0.03092 / 2.06 ( 1149) hydrogen bonds : angle 3.66511 / 2.74 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 1.232 Fit side-chains REVERT: D 218 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 259 PHE cc_start: 0.7980 (m-80) cc_final: 0.7730 (m-80) REVERT: D 454 ASN cc_start: 0.8430 (p0) cc_final: 0.8080 (p0) REVERT: D 523 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7740 (pt) REVERT: D 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8277 (t) REVERT: D 581 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7977 (tpp80) REVERT: C 218 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 259 PHE cc_start: 0.7977 (m-80) cc_final: 0.7729 (m-80) REVERT: C 454 ASN cc_start: 0.8430 (p0) cc_final: 0.8083 (p0) REVERT: C 523 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7735 (pt) REVERT: C 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (t) REVERT: C 581 ARG cc_start: 0.8533 (ttp80) cc_final: 0.7971 (tpp80) REVERT: B 218 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 259 PHE cc_start: 0.7987 (m-80) cc_final: 0.7737 (m-80) REVERT: B 454 ASN cc_start: 0.8415 (p0) cc_final: 0.8065 (p0) REVERT: B 523 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7728 (pt) REVERT: B 524 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8276 (t) REVERT: B 581 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7974 (tpp80) REVERT: A 112 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7507 (mtp180) REVERT: A 218 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 259 PHE cc_start: 0.7976 (m-80) cc_final: 0.7729 (m-80) REVERT: A 287 MET cc_start: 0.7323 (tpp) cc_final: 0.6811 (tpt) REVERT: A 454 ASN cc_start: 0.8422 (p0) cc_final: 0.8073 (p0) REVERT: A 523 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7730 (pt) REVERT: A 524 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8284 (t) REVERT: A 581 ARG cc_start: 0.8535 (ttp80) cc_final: 0.7972 (tpp80) outliers start: 25 outliers final: 12 residues processed: 251 average time/residue: 0.1154 time to fit residues: 45.8690 Evaluate side-chains 255 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128391 restraints weight = 20534.107| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.16 r_work: 0.3352 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17396 Z= 0.112 Angle : 0.520 8.682 23560 Z= 0.247 Chirality : 0.039 0.160 2628 Planarity : 0.003 0.042 2956 Dihedral : 3.827 34.814 2372 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.15 % Allowed : 13.66 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 2116 helix: 2.06 (0.14), residues: 1504 sheet: -0.02 (0.54), residues: 88 loop : -1.42 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.013 0.001 TYR D 411 PHE 0.010 0.001 PHE B 514 TRP 0.019 0.002 TRP A 133 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17396) covalent geometry : angle 0.52030 / 0.25 (23560) hydrogen bonds : bond 0.02956 / 1.97 ( 1149) hydrogen bonds : angle 3.52647 / 2.63 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.601 Fit side-chains REVERT: D 153 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7651 (mtt) REVERT: D 218 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8296 (mp) REVERT: D 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7692 (m-80) REVERT: D 286 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (t-90) REVERT: D 287 MET cc_start: 0.7330 (tpp) cc_final: 0.6802 (tpp) REVERT: D 454 ASN cc_start: 0.8363 (p0) cc_final: 0.8024 (p0) REVERT: D 523 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7688 (pt) REVERT: D 524 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8252 (t) REVERT: D 581 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8074 (tpp80) REVERT: C 153 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7656 (mtt) REVERT: C 218 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 259 PHE cc_start: 0.7948 (m-80) cc_final: 0.7694 (m-80) REVERT: C 286 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: C 287 MET cc_start: 0.7330 (tpp) cc_final: 0.6802 (tpp) REVERT: C 454 ASN cc_start: 0.8361 (p0) cc_final: 0.8026 (p0) REVERT: C 523 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7682 (pt) REVERT: C 524 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 581 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8067 (tpp80) REVERT: B 153 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7648 (mtt) REVERT: B 218 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8297 (mp) REVERT: B 259 PHE cc_start: 0.7949 (m-80) cc_final: 0.7698 (m-80) REVERT: B 286 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: B 287 MET cc_start: 0.7344 (tpp) cc_final: 0.6815 (tpp) REVERT: B 454 ASN cc_start: 0.8342 (p0) cc_final: 0.8004 (p0) REVERT: B 523 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7687 (pt) REVERT: B 524 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8249 (t) REVERT: B 581 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8069 (tpp80) REVERT: A 112 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7388 (ttt-90) REVERT: A 153 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: A 218 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 259 PHE cc_start: 0.7953 (m-80) cc_final: 0.7702 (m-80) REVERT: A 287 MET cc_start: 0.7357 (tpp) cc_final: 0.6821 (tpp) REVERT: A 454 ASN cc_start: 0.8347 (p0) cc_final: 0.8009 (p0) REVERT: A 523 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7684 (pt) REVERT: A 524 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 581 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8067 (tpp80) outliers start: 38 outliers final: 12 residues processed: 271 average time/residue: 0.1028 time to fit residues: 44.1905 Evaluate side-chains 259 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 192 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.170784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123254 restraints weight = 20023.446| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.24 r_work: 0.3340 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17396 Z= 0.116 Angle : 0.533 8.723 23560 Z= 0.254 Chirality : 0.039 0.211 2628 Planarity : 0.003 0.046 2956 Dihedral : 3.780 34.473 2372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.98 % Allowed : 15.02 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 2116 helix: 2.16 (0.14), residues: 1496 sheet: 0.02 (0.54), residues: 88 loop : -1.37 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.012 0.001 TYR A 411 PHE 0.010 0.001 PHE D 514 TRP 0.016 0.002 TRP A 281 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17396) covalent geometry : angle 0.53324 / 0.25 (23560) hydrogen bonds : bond 0.02966 / 1.98 ( 1149) hydrogen bonds : angle 3.49757 / 2.61 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.614 Fit side-chains REVERT: D 218 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 259 PHE cc_start: 0.7935 (m-80) cc_final: 0.7679 (m-80) REVERT: D 286 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: D 287 MET cc_start: 0.7261 (tpp) cc_final: 0.6879 (tpt) REVERT: D 454 ASN cc_start: 0.8360 (p0) cc_final: 0.8031 (p0) REVERT: D 523 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7720 (pt) REVERT: D 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8262 (t) REVERT: D 581 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8072 (tpp80) REVERT: C 218 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8254 (mp) REVERT: C 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7674 (m-80) REVERT: C 286 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7624 (t-90) REVERT: C 287 MET cc_start: 0.7265 (tpp) cc_final: 0.6885 (tpt) REVERT: C 454 ASN cc_start: 0.8359 (p0) cc_final: 0.8032 (p0) REVERT: C 523 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7717 (pt) REVERT: C 524 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 218 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 259 PHE cc_start: 0.7933 (m-80) cc_final: 0.7682 (m-80) REVERT: B 286 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: B 287 MET cc_start: 0.7282 (tpp) cc_final: 0.6902 (tpt) REVERT: B 454 ASN cc_start: 0.8339 (p0) cc_final: 0.8009 (p0) REVERT: B 523 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7721 (pt) REVERT: B 524 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 581 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8071 (tpp80) REVERT: A 112 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7361 (ttt-90) REVERT: A 218 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 259 PHE cc_start: 0.7943 (m-80) cc_final: 0.7688 (m-80) REVERT: A 286 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: A 287 MET cc_start: 0.7319 (tpp) cc_final: 0.6780 (tpp) REVERT: A 454 ASN cc_start: 0.8345 (p0) cc_final: 0.8014 (p0) REVERT: A 523 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7722 (pt) REVERT: A 524 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8262 (t) outliers start: 35 outliers final: 12 residues processed: 249 average time/residue: 0.1027 time to fit residues: 40.5127 Evaluate side-chains 253 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 120 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122069 restraints weight = 20033.225| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.17 r_work: 0.3320 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17396 Z= 0.163 Angle : 0.549 8.824 23560 Z= 0.265 Chirality : 0.041 0.176 2628 Planarity : 0.003 0.049 2956 Dihedral : 3.834 35.667 2372 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 15.53 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2116 helix: 2.11 (0.14), residues: 1496 sheet: 0.04 (0.54), residues: 88 loop : -1.41 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 458 TYR 0.014 0.001 TYR A 411 PHE 0.011 0.001 PHE A 514 TRP 0.017 0.002 TRP B 281 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (17396) covalent geometry : angle 0.54936 / 0.26 (23560) hydrogen bonds : bond 0.03258 / 2.17 ( 1149) hydrogen bonds : angle 3.55203 / 2.65 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.662 Fit side-chains REVERT: D 218 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8339 (mp) REVERT: D 259 PHE cc_start: 0.7901 (m-80) cc_final: 0.7663 (m-80) REVERT: D 287 MET cc_start: 0.6946 (tpp) cc_final: 0.6713 (tpp) REVERT: D 523 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7674 (pt) REVERT: D 524 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8267 (t) REVERT: D 581 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8078 (tpp80) REVERT: C 218 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8328 (mp) REVERT: C 259 PHE cc_start: 0.7896 (m-80) cc_final: 0.7658 (m-80) REVERT: C 287 MET cc_start: 0.6940 (tpp) cc_final: 0.6707 (tpp) REVERT: C 523 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7673 (pt) REVERT: C 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 581 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8076 (tpp80) REVERT: B 218 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 259 PHE cc_start: 0.7900 (m-80) cc_final: 0.7664 (m-80) REVERT: B 287 MET cc_start: 0.6958 (tpp) cc_final: 0.6724 (tpp) REVERT: B 523 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (pt) REVERT: B 524 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 581 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8074 (tpp80) REVERT: A 112 ARG cc_start: 0.7821 (mtp180) cc_final: 0.7533 (ttt-90) REVERT: A 218 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 259 PHE cc_start: 0.7904 (m-80) cc_final: 0.7669 (m-80) REVERT: A 286 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: A 287 MET cc_start: 0.7266 (tpp) cc_final: 0.6702 (tpp) REVERT: A 523 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7673 (pt) REVERT: A 524 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8270 (t) outliers start: 25 outliers final: 12 residues processed: 254 average time/residue: 0.1133 time to fit residues: 44.4650 Evaluate side-chains 248 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 3 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120785 restraints weight = 20275.527| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.26 r_work: 0.3294 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17396 Z= 0.184 Angle : 0.578 8.867 23560 Z= 0.278 Chirality : 0.041 0.170 2628 Planarity : 0.004 0.050 2956 Dihedral : 3.877 36.502 2372 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.04 % Allowed : 15.53 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2116 helix: 2.04 (0.14), residues: 1500 sheet: 0.01 (0.53), residues: 88 loop : -1.39 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.014 0.001 TYR C 411 PHE 0.011 0.001 PHE D 514 TRP 0.018 0.002 TRP B 281 HIS 0.004 0.001 HIS D 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (17396) covalent geometry : angle 0.57753 / 0.28 (23560) hydrogen bonds : bond 0.03376 / 2.25 ( 1149) hydrogen bonds : angle 3.60527 / 2.69 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.555 Fit side-chains REVERT: D 218 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8361 (mp) REVERT: D 259 PHE cc_start: 0.7919 (m-80) cc_final: 0.7681 (m-80) REVERT: D 287 MET cc_start: 0.7077 (tpp) cc_final: 0.6854 (tpt) REVERT: D 523 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7625 (pt) REVERT: D 524 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8262 (t) REVERT: D 540 GLU cc_start: 0.7629 (pm20) cc_final: 0.7364 (pm20) REVERT: D 581 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8114 (tpp80) REVERT: C 218 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 259 PHE cc_start: 0.7919 (m-80) cc_final: 0.7678 (m-80) REVERT: C 287 MET cc_start: 0.7066 (tpp) cc_final: 0.6844 (tpt) REVERT: C 523 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7611 (pt) REVERT: C 524 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (t) REVERT: C 540 GLU cc_start: 0.7636 (pm20) cc_final: 0.7365 (pm20) REVERT: C 581 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8115 (tpp80) REVERT: B 218 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 259 PHE cc_start: 0.7927 (m-80) cc_final: 0.7688 (m-80) REVERT: B 287 MET cc_start: 0.7085 (tpp) cc_final: 0.6860 (tpt) REVERT: B 523 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7626 (pt) REVERT: B 524 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8260 (t) REVERT: B 540 GLU cc_start: 0.7647 (pm20) cc_final: 0.7382 (pm20) REVERT: B 581 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8113 (tpp80) REVERT: A 112 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7532 (ttt-90) REVERT: A 218 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 259 PHE cc_start: 0.7926 (m-80) cc_final: 0.7689 (m-80) REVERT: A 286 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7646 (t-90) REVERT: A 287 MET cc_start: 0.7341 (tpp) cc_final: 0.6801 (tpp) REVERT: A 523 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7612 (pt) REVERT: A 524 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 540 GLU cc_start: 0.7651 (pm20) cc_final: 0.7384 (pm20) REVERT: A 581 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8113 (tpp80) outliers start: 36 outliers final: 16 residues processed: 260 average time/residue: 0.1066 time to fit residues: 43.7908 Evaluate side-chains 255 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 22 optimal weight: 0.0010 chunk 172 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124504 restraints weight = 20088.377| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.18 r_work: 0.3345 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17396 Z= 0.112 Angle : 0.555 8.641 23560 Z= 0.265 Chirality : 0.039 0.168 2628 Planarity : 0.003 0.042 2956 Dihedral : 3.803 35.627 2372 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.76 % Allowed : 15.59 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 2116 helix: 2.20 (0.14), residues: 1500 sheet: 0.02 (0.54), residues: 88 loop : -1.34 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.012 0.001 TYR C 411 PHE 0.010 0.001 PHE B 514 TRP 0.017 0.001 TRP A 133 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17396) covalent geometry : angle 0.55533 / 0.27 (23560) hydrogen bonds : bond 0.02912 / 1.95 ( 1149) hydrogen bonds : angle 3.48057 / 2.60 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.520 Fit side-chains REVERT: D 112 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7640 (mmm-85) REVERT: D 218 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8392 (mp) REVERT: D 259 PHE cc_start: 0.7911 (m-80) cc_final: 0.7668 (m-80) REVERT: D 523 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7685 (pt) REVERT: D 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (t) REVERT: D 540 GLU cc_start: 0.7513 (pm20) cc_final: 0.7247 (pm20) REVERT: D 581 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8085 (tpp80) REVERT: C 112 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7635 (mmm-85) REVERT: C 218 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 259 PHE cc_start: 0.7909 (m-80) cc_final: 0.7665 (m-80) REVERT: C 523 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7669 (pt) REVERT: C 524 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8270 (t) REVERT: C 540 GLU cc_start: 0.7538 (pm20) cc_final: 0.7270 (pm20) REVERT: C 581 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8091 (tpp80) REVERT: B 112 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7640 (mmm-85) REVERT: B 218 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 259 PHE cc_start: 0.7915 (m-80) cc_final: 0.7674 (m-80) REVERT: B 523 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7670 (pt) REVERT: B 524 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8270 (t) REVERT: B 540 GLU cc_start: 0.7546 (pm20) cc_final: 0.7279 (pm20) REVERT: B 581 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8084 (tpp80) REVERT: A 218 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 259 PHE cc_start: 0.7923 (m-80) cc_final: 0.7681 (m-80) REVERT: A 286 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7614 (t-90) REVERT: A 287 MET cc_start: 0.7400 (tpp) cc_final: 0.6891 (tpp) REVERT: A 523 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7680 (pt) REVERT: A 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (t) REVERT: A 540 GLU cc_start: 0.7541 (pm20) cc_final: 0.7277 (pm20) outliers start: 31 outliers final: 17 residues processed: 259 average time/residue: 0.1005 time to fit residues: 41.3315 Evaluate side-chains 259 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124318 restraints weight = 19962.312| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.24 r_work: 0.3343 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17396 Z= 0.116 Angle : 0.570 8.786 23560 Z= 0.270 Chirality : 0.039 0.164 2628 Planarity : 0.003 0.042 2956 Dihedral : 3.762 32.898 2372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.15 % Allowed : 15.19 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2116 helix: 2.21 (0.14), residues: 1500 sheet: 0.01 (0.54), residues: 88 loop : -1.29 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.012 0.001 TYR D 411 PHE 0.010 0.001 PHE D 514 TRP 0.016 0.001 TRP D 281 HIS 0.003 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17396) covalent geometry : angle 0.56954 / 0.27 (23560) hydrogen bonds : bond 0.02883 / 1.93 ( 1149) hydrogen bonds : angle 3.45874 / 2.58 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.526 Fit side-chains REVERT: D 218 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8363 (mp) REVERT: D 259 PHE cc_start: 0.7902 (m-80) cc_final: 0.7646 (m-80) REVERT: D 287 MET cc_start: 0.7107 (tpp) cc_final: 0.6702 (tpt) REVERT: D 523 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7819 (pt) REVERT: D 524 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8293 (t) REVERT: D 540 GLU cc_start: 0.7552 (pm20) cc_final: 0.7279 (pm20) REVERT: D 581 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8104 (tpp80) REVERT: C 218 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 259 PHE cc_start: 0.7890 (m-80) cc_final: 0.7636 (m-80) REVERT: C 287 MET cc_start: 0.7094 (tpp) cc_final: 0.6691 (tpt) REVERT: C 523 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7802 (pt) REVERT: C 524 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 540 GLU cc_start: 0.7568 (pm20) cc_final: 0.7295 (pm20) REVERT: C 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8101 (tpp80) REVERT: B 218 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 259 PHE cc_start: 0.7901 (m-80) cc_final: 0.7651 (m-80) REVERT: B 287 MET cc_start: 0.7114 (tpp) cc_final: 0.6709 (tpt) REVERT: B 523 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7801 (pt) REVERT: B 524 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 540 GLU cc_start: 0.7589 (pm20) cc_final: 0.7316 (pm20) REVERT: B 581 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8103 (tpp80) REVERT: A 112 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7539 (ttt-90) REVERT: A 218 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 259 PHE cc_start: 0.7913 (m-80) cc_final: 0.7663 (m-80) REVERT: A 286 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7567 (t-90) REVERT: A 287 MET cc_start: 0.7414 (tpp) cc_final: 0.6985 (tpp) REVERT: A 523 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7815 (pt) REVERT: A 524 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8294 (t) REVERT: A 540 GLU cc_start: 0.7577 (pm20) cc_final: 0.7306 (pm20) REVERT: A 581 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8112 (tpp80) outliers start: 38 outliers final: 17 residues processed: 261 average time/residue: 0.0997 time to fit residues: 41.4012 Evaluate side-chains 263 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 199 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.165577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117909 restraints weight = 20241.045| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.16 r_work: 0.3262 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 17396 Z= 0.314 Angle : 0.678 9.322 23560 Z= 0.338 Chirality : 0.045 0.225 2628 Planarity : 0.004 0.061 2956 Dihedral : 4.092 36.754 2372 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.76 % Allowed : 14.74 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 2116 helix: 1.73 (0.13), residues: 1500 sheet: -0.04 (0.54), residues: 88 loop : -1.48 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 458 TYR 0.019 0.002 TYR D 411 PHE 0.013 0.002 PHE D 514 TRP 0.020 0.002 TRP A 281 HIS 0.004 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.31 (17396) covalent geometry : angle 0.67805 / 0.34 (23560) hydrogen bonds : bond 0.04033 / 2.68 ( 1149) hydrogen bonds : angle 3.78450 / 2.83 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4137.58 seconds wall clock time: 71 minutes 24.67 seconds (4284.67 seconds total)