Starting phenix.real_space_refine on Sun Aug 24 04:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_41036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_41036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_41036.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_41036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4m_41036/08_2025/8t4m_41036.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: C, B, A Time building chain proxies: 3.63, per 1000 atoms: 0.21 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: 1.64 Conformation dependent library (CDL) restraints added in 670.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.64 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: 3.11 Time building geometry restraints manager: 2.10 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=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+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: 23320 2.29 - 4.58: 188 4.58 - 6.87: 36 6.87 - 9.16: 12 9.16 - 11.45: 4 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 - 26.04: 9800 26.04 - 52.07: 500 52.07 - 78.11: 52 78.11 - 104.14: 4 104.14 - 130.18: 4 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 - 0.024: 1551 0.024 - 0.049: 581 0.049 - 0.073: 348 0.073 - 0.097: 84 0.097 - 0.122: 64 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (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: 1.840 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.430 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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= 0.111 Angle : 0.565 11.451 23560 Z= 0.283 Chirality : 0.037 0.122 2628 Planarity : 0.003 0.044 2956 Dihedral : 14.873 130.178 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 aren 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 covalent geometry : bond 0.00217 (17396) covalent geometry : angle 0.56460 (23560) hydrogen bonds : bond 0.09890 ( 1149) hydrogen bonds : angle 4.35095 ( 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 : 0.485 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: 0.1262 time to fit residues: 53.7324 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 : 0.615 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4085 r_free = 0.4085 target = 0.176378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129004 restraints weight = 20446.873| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.26 r_work: 0.3345 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0880 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= 0.149 Angle : 0.524 7.711 23560 Z= 0.266 Chirality : 0.040 0.172 2628 Planarity : 0.004 0.034 2956 Dihedral : 6.799 131.970 2372 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 13.61 % Favored : 85.03 % 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 aren not related in a simple way. whole: 1.41 (0.19), residues: 2116 helix: 1.78 (0.14), residues: 1504 sheet: -0.09 (0.55), residues: 88 loop : -1.40 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 590 TYR 0.012 0.001 TYR B 411 PHE 0.008 0.001 PHE B 514 TRP 0.018 0.002 TRP A 281 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00345 (17396) covalent geometry : angle 0.52393 (23560) hydrogen bonds : bond 0.03342 ( 1149) hydrogen bonds : angle 3.67839 ( 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 : 0.654 Fit side-chains REVERT: D 259 PHE cc_start: 0.7942 (m-80) cc_final: 0.7701 (m-80) REVERT: D 286 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7493 (t-90) REVERT: D 287 MET cc_start: 0.7404 (tpp) cc_final: 0.7196 (tpp) REVERT: D 524 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8059 (p) REVERT: D 581 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7949 (tpp80) REVERT: C 259 PHE cc_start: 0.7942 (m-80) cc_final: 0.7701 (m-80) REVERT: C 286 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: C 287 MET cc_start: 0.7403 (tpp) cc_final: 0.7191 (tpp) REVERT: C 524 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8054 (p) REVERT: C 581 ARG cc_start: 0.8530 (ttp80) cc_final: 0.7954 (tpp80) REVERT: B 259 PHE cc_start: 0.7947 (m-80) cc_final: 0.7708 (m-80) REVERT: B 286 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (t-90) REVERT: B 287 MET cc_start: 0.7400 (tpp) cc_final: 0.7193 (tpp) REVERT: B 524 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8048 (p) REVERT: B 581 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7959 (tpp80) REVERT: A 259 PHE cc_start: 0.7953 (m-80) cc_final: 0.7715 (m-80) REVERT: A 286 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7493 (t-90) REVERT: A 287 MET cc_start: 0.7411 (tpp) cc_final: 0.7204 (tpp) REVERT: A 524 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 581 ARG cc_start: 0.8532 (ttp80) cc_final: 0.7962 (tpp80) outliers start: 24 outliers final: 4 residues processed: 268 average time/residue: 0.1078 time to fit residues: 45.1790 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 : 0.474 ------------------------------------------------------------------------------- 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: 3.9990 chunk 208 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3992 r_free = 0.3992 target = 0.165510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117373 restraints weight = 20684.156| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.20 r_work: 0.3252 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 17396 Z= 0.328 Angle : 0.640 8.173 23560 Z= 0.334 Chirality : 0.046 0.181 2628 Planarity : 0.005 0.053 2956 Dihedral : 6.924 130.357 2372 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.21 % Allowed : 13.89 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2116 helix: 1.49 (0.13), residues: 1496 sheet: 0.02 (0.54), residues: 88 loop : -1.62 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 112 TYR 0.018 0.002 TYR B 411 PHE 0.011 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 covalent geometry : bond 0.00798 (17396) covalent geometry : angle 0.64028 (23560) hydrogen bonds : bond 0.04350 ( 1149) hydrogen bonds : angle 3.94577 ( 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 267 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.701 Fit side-chains REVERT: D 259 PHE cc_start: 0.7894 (m-80) cc_final: 0.7419 (m-80) REVERT: D 287 MET cc_start: 0.7470 (tpp) cc_final: 0.6889 (tpp) REVERT: D 524 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (t) REVERT: D 581 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7975 (tpp80) REVERT: C 259 PHE cc_start: 0.7890 (m-80) cc_final: 0.7413 (m-80) REVERT: C 287 MET cc_start: 0.7484 (tpp) cc_final: 0.6903 (tpp) REVERT: C 524 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8369 (t) REVERT: C 581 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7967 (tpp80) REVERT: B 259 PHE cc_start: 0.7899 (m-80) cc_final: 0.7422 (m-80) REVERT: B 287 MET cc_start: 0.7478 (tpp) cc_final: 0.6894 (tpp) REVERT: B 524 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8367 (t) REVERT: B 581 ARG cc_start: 0.8540 (ttp80) cc_final: 0.7977 (tpp80) REVERT: A 259 PHE cc_start: 0.7901 (m-80) cc_final: 0.7427 (m-80) REVERT: A 287 MET cc_start: 0.7482 (tpp) cc_final: 0.6901 (tpp) REVERT: A 524 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 581 ARG cc_start: 0.8529 (ttp80) cc_final: 0.7969 (tpp80) outliers start: 39 outliers final: 19 residues processed: 248 average time/residue: 0.1098 time to fit residues: 42.9028 Evaluate side-chains 231 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121595 restraints weight = 20087.105| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.23 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17396 Z= 0.119 Angle : 0.506 7.471 23560 Z= 0.260 Chirality : 0.039 0.182 2628 Planarity : 0.003 0.043 2956 Dihedral : 6.912 132.355 2372 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.19 % Allowed : 14.91 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.19), residues: 2116 helix: 1.91 (0.14), residues: 1496 sheet: -0.08 (0.54), residues: 88 loop : -1.54 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 467 TYR 0.016 0.001 TYR B 411 PHE 0.009 0.001 PHE B 514 TRP 0.017 0.002 TRP D 281 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00263 (17396) covalent geometry : angle 0.50554 (23560) hydrogen bonds : bond 0.03173 ( 1149) hydrogen bonds : angle 3.71648 ( 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 245 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 218 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 259 PHE cc_start: 0.7886 (m-80) cc_final: 0.7667 (m-80) REVERT: D 454 ASN cc_start: 0.8472 (p0) cc_final: 0.8105 (p0) REVERT: D 523 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7575 (pt) REVERT: D 524 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (t) REVERT: D 581 ARG cc_start: 0.8548 (ttp80) cc_final: 0.7967 (tpp80) REVERT: C 218 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 259 PHE cc_start: 0.7885 (m-80) cc_final: 0.7668 (m-80) REVERT: C 454 ASN cc_start: 0.8472 (p0) cc_final: 0.8107 (p0) REVERT: C 523 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7562 (pt) REVERT: C 524 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 581 ARG cc_start: 0.8545 (ttp80) cc_final: 0.7960 (tpp80) REVERT: B 218 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 259 PHE cc_start: 0.7895 (m-80) cc_final: 0.7676 (m-80) REVERT: B 454 ASN cc_start: 0.8462 (p0) cc_final: 0.8095 (p0) REVERT: B 523 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7563 (pt) REVERT: B 524 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 581 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7963 (tpp80) REVERT: A 218 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 259 PHE cc_start: 0.7889 (m-80) cc_final: 0.7673 (m-80) REVERT: A 454 ASN cc_start: 0.8465 (p0) cc_final: 0.8099 (p0) REVERT: A 523 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7552 (pt) REVERT: A 524 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8285 (t) REVERT: A 581 ARG cc_start: 0.8547 (ttp80) cc_final: 0.7968 (tpp80) outliers start: 21 outliers final: 9 residues processed: 240 average time/residue: 0.1132 time to fit residues: 42.7940 Evaluate side-chains 241 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 164 ILE 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 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 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 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: 0.5980 chunk 146 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122856 restraints weight = 20067.872| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.23 r_work: 0.3333 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1461 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 : 0.492 7.548 23560 Z= 0.250 Chirality : 0.039 0.162 2628 Planarity : 0.003 0.042 2956 Dihedral : 6.856 132.597 2372 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.87 % Allowed : 14.46 % Favored : 83.67 % 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 aren not related in a simple way. whole: 1.72 (0.19), residues: 2116 helix: 2.04 (0.14), residues: 1500 sheet: -0.01 (0.54), residues: 88 loop : -1.35 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.013 0.001 TYR A 411 PHE 0.010 0.001 PHE B 514 TRP 0.018 0.002 TRP A 133 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00258 (17396) covalent geometry : angle 0.49250 (23560) hydrogen bonds : bond 0.02947 ( 1149) hydrogen bonds : angle 3.57832 ( 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 277 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 LYS cc_start: 0.7894 (tptt) cc_final: 0.7601 (tptt) REVERT: D 153 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: D 218 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8300 (mp) REVERT: D 259 PHE cc_start: 0.7889 (m-80) cc_final: 0.7660 (m-80) REVERT: D 454 ASN cc_start: 0.8390 (p0) cc_final: 0.8054 (p0) REVERT: D 523 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7605 (pt) REVERT: D 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 581 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8053 (tpp80) REVERT: C 108 LYS cc_start: 0.7869 (tptt) cc_final: 0.7573 (tptt) REVERT: C 153 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7716 (mtt) REVERT: C 218 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8300 (mp) REVERT: C 259 PHE cc_start: 0.7893 (m-80) cc_final: 0.7663 (m-80) REVERT: C 454 ASN cc_start: 0.8391 (p0) cc_final: 0.8057 (p0) REVERT: C 523 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7597 (pt) REVERT: C 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8256 (t) REVERT: C 581 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8053 (tpp80) REVERT: B 108 LYS cc_start: 0.7863 (tptt) cc_final: 0.7568 (tptt) REVERT: B 153 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7710 (mtt) REVERT: B 218 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 259 PHE cc_start: 0.7891 (m-80) cc_final: 0.7662 (m-80) REVERT: B 454 ASN cc_start: 0.8386 (p0) cc_final: 0.8052 (p0) REVERT: B 523 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7600 (pt) REVERT: B 524 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 581 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8051 (tpp80) REVERT: A 108 LYS cc_start: 0.7873 (tptt) cc_final: 0.7581 (tptt) REVERT: A 153 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7707 (mtt) REVERT: A 218 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 259 PHE cc_start: 0.7892 (m-80) cc_final: 0.7663 (m-80) REVERT: A 454 ASN cc_start: 0.8386 (p0) cc_final: 0.8051 (p0) REVERT: A 523 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7592 (pt) REVERT: A 524 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8258 (t) REVERT: A 581 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8054 (tpp80) outliers start: 33 outliers final: 12 residues processed: 268 average time/residue: 0.1221 time to fit residues: 51.5796 Evaluate side-chains 268 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 146 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121385 restraints weight = 20029.680| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.23 r_work: 0.3315 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17396 Z= 0.150 Angle : 0.510 7.617 23560 Z= 0.260 Chirality : 0.040 0.202 2628 Planarity : 0.003 0.048 2956 Dihedral : 6.838 132.227 2372 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.81 % Allowed : 14.68 % 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 aren not related in a simple way. whole: 1.74 (0.19), residues: 2116 helix: 2.07 (0.14), residues: 1496 sheet: 0.09 (0.54), residues: 88 loop : -1.37 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 458 TYR 0.014 0.001 TYR C 411 PHE 0.011 0.001 PHE B 514 TRP 0.018 0.002 TRP C 133 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00352 (17396) covalent geometry : angle 0.50993 (23560) hydrogen bonds : bond 0.03101 ( 1149) hydrogen bonds : angle 3.58817 ( 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 268 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.651 Fit side-chains REVERT: D 218 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8302 (mp) REVERT: D 259 PHE cc_start: 0.7908 (m-80) cc_final: 0.7676 (m-80) REVERT: D 287 MET cc_start: 0.7180 (tpp) cc_final: 0.6850 (tpt) REVERT: D 454 ASN cc_start: 0.8473 (p0) cc_final: 0.8120 (p0) REVERT: D 523 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7610 (pt) REVERT: D 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8263 (t) REVERT: D 581 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8069 (tpp80) REVERT: C 218 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 259 PHE cc_start: 0.7901 (m-80) cc_final: 0.7671 (m-80) REVERT: C 287 MET cc_start: 0.7174 (tpp) cc_final: 0.6838 (tpt) REVERT: C 454 ASN cc_start: 0.8477 (p0) cc_final: 0.8125 (p0) REVERT: C 523 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7603 (pt) REVERT: C 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8261 (t) REVERT: C 581 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8069 (tpp80) REVERT: B 218 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 259 PHE cc_start: 0.7906 (m-80) cc_final: 0.7675 (m-80) REVERT: B 287 MET cc_start: 0.7183 (tpp) cc_final: 0.6850 (tpt) REVERT: B 454 ASN cc_start: 0.8466 (p0) cc_final: 0.8112 (p0) REVERT: B 523 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7595 (pt) REVERT: B 524 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8249 (t) REVERT: B 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8068 (tpp80) REVERT: A 218 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 259 PHE cc_start: 0.7911 (m-80) cc_final: 0.7680 (m-80) REVERT: A 287 MET cc_start: 0.7186 (tpp) cc_final: 0.6848 (tpt) REVERT: A 454 ASN cc_start: 0.8473 (p0) cc_final: 0.8121 (p0) REVERT: A 523 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7598 (pt) REVERT: A 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8255 (t) REVERT: A 581 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8067 (tpp80) outliers start: 32 outliers final: 16 residues processed: 260 average time/residue: 0.0997 time to fit residues: 41.5037 Evaluate side-chains 256 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 162 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122363 restraints weight = 19933.078| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.23 r_work: 0.3330 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1583 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= 0.128 Angle : 0.498 7.598 23560 Z= 0.252 Chirality : 0.039 0.178 2628 Planarity : 0.003 0.047 2956 Dihedral : 6.833 132.447 2372 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 15.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.19), residues: 2116 helix: 2.10 (0.14), residues: 1504 sheet: 0.09 (0.54), residues: 88 loop : -1.33 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 467 TYR 0.013 0.001 TYR B 411 PHE 0.010 0.001 PHE B 514 TRP 0.021 0.002 TRP D 133 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00294 (17396) covalent geometry : angle 0.49848 (23560) hydrogen bonds : bond 0.02947 ( 1149) hydrogen bonds : angle 3.54195 ( 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 264 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.678 Fit side-chains REVERT: D 218 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8233 (mp) REVERT: D 259 PHE cc_start: 0.7895 (m-80) cc_final: 0.7658 (m-80) REVERT: D 287 MET cc_start: 0.7091 (tpp) cc_final: 0.6878 (tpt) REVERT: D 454 ASN cc_start: 0.8416 (p0) cc_final: 0.8081 (p0) REVERT: D 523 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7644 (pt) REVERT: D 524 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8259 (t) REVERT: C 218 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 259 PHE cc_start: 0.7896 (m-80) cc_final: 0.7661 (m-80) REVERT: C 287 MET cc_start: 0.7089 (tpp) cc_final: 0.6869 (tpt) REVERT: C 454 ASN cc_start: 0.8422 (p0) cc_final: 0.8089 (p0) REVERT: C 523 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7642 (pt) REVERT: C 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8259 (t) REVERT: B 218 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 259 PHE cc_start: 0.7897 (m-80) cc_final: 0.7663 (m-80) REVERT: B 287 MET cc_start: 0.7089 (tpp) cc_final: 0.6877 (tpt) REVERT: B 454 ASN cc_start: 0.8412 (p0) cc_final: 0.8080 (p0) REVERT: B 523 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7621 (pt) REVERT: B 524 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 218 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 259 PHE cc_start: 0.7899 (m-80) cc_final: 0.7664 (m-80) REVERT: A 287 MET cc_start: 0.7099 (tpp) cc_final: 0.6880 (tpt) REVERT: A 454 ASN cc_start: 0.8416 (p0) cc_final: 0.8080 (p0) REVERT: A 523 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7634 (pt) REVERT: A 524 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8254 (t) outliers start: 36 outliers final: 16 residues processed: 252 average time/residue: 0.1146 time to fit residues: 46.5411 Evaluate side-chains 252 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128257 restraints weight = 20461.668| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.23 r_work: 0.3424 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17396 Z= 0.130 Angle : 0.519 8.084 23560 Z= 0.259 Chirality : 0.039 0.168 2628 Planarity : 0.003 0.047 2956 Dihedral : 6.840 132.992 2372 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.27 % Allowed : 15.42 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.90 (0.19), residues: 2116 helix: 2.20 (0.14), residues: 1496 sheet: 0.10 (0.54), residues: 88 loop : -1.33 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.013 0.001 TYR B 411 PHE 0.011 0.001 PHE B 514 TRP 0.021 0.002 TRP D 133 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00300 (17396) covalent geometry : angle 0.51949 (23560) hydrogen bonds : bond 0.02948 ( 1149) hydrogen bonds : angle 3.52643 ( 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 272 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.699 Fit side-chains REVERT: D 218 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8517 (mp) REVERT: D 259 PHE cc_start: 0.8034 (m-80) cc_final: 0.7774 (m-80) REVERT: D 454 ASN cc_start: 0.8472 (p0) cc_final: 0.8154 (p0) REVERT: D 523 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7867 (pt) REVERT: D 524 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8324 (t) REVERT: C 218 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 259 PHE cc_start: 0.8028 (m-80) cc_final: 0.7770 (m-80) REVERT: C 454 ASN cc_start: 0.8476 (p0) cc_final: 0.8160 (p0) REVERT: C 523 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7859 (pt) REVERT: C 524 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8317 (t) REVERT: B 218 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 259 PHE cc_start: 0.8033 (m-80) cc_final: 0.7775 (m-80) REVERT: B 454 ASN cc_start: 0.8464 (p0) cc_final: 0.8148 (p0) REVERT: B 523 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7853 (pt) REVERT: B 524 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 108 LYS cc_start: 0.7945 (tptt) cc_final: 0.7737 (tptt) REVERT: A 218 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 259 PHE cc_start: 0.8032 (m-80) cc_final: 0.7774 (m-80) REVERT: A 454 ASN cc_start: 0.8465 (p0) cc_final: 0.8147 (p0) REVERT: A 523 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 524 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8315 (t) outliers start: 40 outliers final: 16 residues processed: 260 average time/residue: 0.1164 time to fit residues: 48.8868 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 : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 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 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 113 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 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 113 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 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 113 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121689 restraints weight = 20176.600| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.25 r_work: 0.3324 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17396 Z= 0.151 Angle : 0.560 7.874 23560 Z= 0.285 Chirality : 0.040 0.224 2628 Planarity : 0.004 0.054 2956 Dihedral : 6.824 132.015 2372 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.27 % Allowed : 15.42 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.87 (0.19), residues: 2116 helix: 2.15 (0.14), residues: 1496 sheet: 0.11 (0.54), residues: 88 loop : -1.27 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 112 TYR 0.013 0.001 TYR B 411 PHE 0.011 0.001 PHE B 514 TRP 0.023 0.002 TRP D 133 HIS 0.004 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00353 (17396) covalent geometry : angle 0.55964 (23560) hydrogen bonds : bond 0.03051 ( 1149) hydrogen bonds : angle 3.59757 ( 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 269 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.687 Fit side-chains REVERT: D 218 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8253 (mp) REVERT: D 259 PHE cc_start: 0.7902 (m-80) cc_final: 0.7664 (m-80) REVERT: D 454 ASN cc_start: 0.8473 (p0) cc_final: 0.8134 (p0) REVERT: D 523 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7692 (pt) REVERT: D 524 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8260 (t) REVERT: C 218 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8244 (mp) REVERT: C 259 PHE cc_start: 0.7897 (m-80) cc_final: 0.7661 (m-80) REVERT: C 454 ASN cc_start: 0.8481 (p0) cc_final: 0.8143 (p0) REVERT: C 523 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7685 (pt) REVERT: C 524 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 218 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 259 PHE cc_start: 0.7901 (m-80) cc_final: 0.7665 (m-80) REVERT: B 454 ASN cc_start: 0.8472 (p0) cc_final: 0.8133 (p0) REVERT: B 523 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7673 (pt) REVERT: B 524 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 218 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 259 PHE cc_start: 0.7903 (m-80) cc_final: 0.7668 (m-80) REVERT: A 454 ASN cc_start: 0.8478 (p0) cc_final: 0.8138 (p0) REVERT: A 523 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7673 (pt) REVERT: A 524 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8253 (t) outliers start: 40 outliers final: 16 residues processed: 253 average time/residue: 0.1153 time to fit residues: 46.9534 Evaluate side-chains 252 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.170551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123047 restraints weight = 19914.306| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.22 r_work: 0.3342 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17396 Z= 0.125 Angle : 0.547 7.807 23560 Z= 0.276 Chirality : 0.039 0.207 2628 Planarity : 0.004 0.052 2956 Dihedral : 6.821 132.476 2372 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 16.04 % Favored : 81.92 % 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 aren not related in a simple way. whole: 1.92 (0.19), residues: 2116 helix: 2.19 (0.14), residues: 1500 sheet: 0.11 (0.54), residues: 88 loop : -1.29 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 467 TYR 0.012 0.001 TYR D 411 PHE 0.010 0.001 PHE B 514 TRP 0.024 0.002 TRP D 133 HIS 0.004 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00281 (17396) covalent geometry : angle 0.54701 (23560) hydrogen bonds : bond 0.02882 ( 1149) hydrogen bonds : angle 3.55763 ( 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 275 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.676 Fit side-chains REVERT: D 218 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8395 (mp) REVERT: D 259 PHE cc_start: 0.7900 (m-80) cc_final: 0.7652 (m-80) REVERT: D 286 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: D 454 ASN cc_start: 0.8331 (p0) cc_final: 0.8024 (p0) REVERT: D 523 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7773 (pt) REVERT: D 524 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8289 (t) REVERT: C 218 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 259 PHE cc_start: 0.7885 (m-80) cc_final: 0.7640 (m-80) REVERT: C 286 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7231 (t-90) REVERT: C 287 MET cc_start: 0.7413 (tpp) cc_final: 0.7205 (tpp) REVERT: C 454 ASN cc_start: 0.8329 (p0) cc_final: 0.8028 (p0) REVERT: C 523 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7768 (pt) REVERT: C 524 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8275 (t) REVERT: B 218 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8387 (mp) REVERT: B 259 PHE cc_start: 0.7890 (m-80) cc_final: 0.7646 (m-80) REVERT: B 286 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7242 (t-90) REVERT: B 287 MET cc_start: 0.7429 (tpp) cc_final: 0.7224 (tpp) REVERT: B 454 ASN cc_start: 0.8314 (p0) cc_final: 0.8010 (p0) REVERT: B 523 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7754 (pt) REVERT: B 524 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 218 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 259 PHE cc_start: 0.7897 (m-80) cc_final: 0.7652 (m-80) REVERT: A 286 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: A 523 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7748 (pt) REVERT: A 524 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8270 (t) outliers start: 36 outliers final: 16 residues processed: 263 average time/residue: 0.1163 time to fit residues: 49.4123 Evaluate side-chains 268 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 232 VAL 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 232 VAL 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 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: 0.9980 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118939 restraints weight = 20022.187| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.22 r_work: 0.3290 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17396 Z= 0.209 Angle : 0.585 8.022 23560 Z= 0.299 Chirality : 0.042 0.200 2628 Planarity : 0.004 0.059 2956 Dihedral : 6.845 131.436 2372 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % 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 aren not related in a simple way. whole: 1.68 (0.19), residues: 2116 helix: 2.02 (0.14), residues: 1492 sheet: 0.11 (0.54), residues: 88 loop : -1.37 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 112 TYR 0.015 0.002 TYR A 411 PHE 0.012 0.001 PHE C 514 TRP 0.021 0.002 TRP D 133 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00501 (17396) covalent geometry : angle 0.58460 (23560) hydrogen bonds : bond 0.03405 ( 1149) hydrogen bonds : angle 3.67317 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.59 seconds wall clock time: 79 minutes 25.84 seconds (4765.84 seconds total)