Starting phenix.real_space_refine on Sun May 18 12:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4m_41036/05_2025/8t4m_41036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4m_41036/05_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_41036/05_2025/8t4m_41036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4m_41036/05_2025/8t4m_41036.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4m_41036/05_2025/8t4m_41036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4m_41036/05_2025/8t4m_41036.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "A" 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, D Time building chain proxies: 9.10, per 1000 atoms: 0.54 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: 4.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.94 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: 5.45 Time building geometry restraints manager: 4.76 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (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 TRP 0.025 0.002 TRP B 133 HIS 0.002 0.001 HIS C 421 PHE 0.005 0.001 PHE A 483 TYR 0.014 0.001 TYR D 576 ARG 0.002 0.000 ARG D 467 Details of bonding type rmsd hydrogen bonds : bond 0.09890 ( 1149) hydrogen bonds : angle 4.35095 ( 3363) covalent geometry : bond 0.00217 (17396) covalent geometry : angle 0.56460 (23560) *********************** 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 : 1.785 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: 0.2864 time to fit residues: 121.4977 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 : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.173791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127354 restraints weight = 20299.623| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.14 r_work: 0.3424 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17396 Z= 0.188 Angle : 0.550 7.756 23560 Z= 0.282 Chirality : 0.041 0.174 2628 Planarity : 0.004 0.039 2956 Dihedral : 6.825 131.657 2372 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.13 % Allowed : 14.06 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 2116 helix: 1.70 (0.13), residues: 1500 sheet: -0.18 (0.55), residues: 88 loop : -1.45 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 PHE 0.008 0.001 PHE B 514 TYR 0.013 0.001 TYR B 411 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 1149) hydrogen bonds : angle 3.71739 ( 3363) covalent geometry : bond 0.00445 (17396) covalent geometry : angle 0.54985 (23560) *********************** 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 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 2.036 Fit side-chains REVERT: D 108 LYS cc_start: 0.7824 (tptt) cc_final: 0.7483 (tptt) REVERT: D 259 PHE cc_start: 0.8021 (m-80) cc_final: 0.7774 (m-80) REVERT: D 286 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7511 (t-90) REVERT: D 524 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8128 (p) REVERT: D 581 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7960 (tpp80) REVERT: C 108 LYS cc_start: 0.7827 (tptt) cc_final: 0.7483 (tptt) REVERT: C 259 PHE cc_start: 0.8024 (m-80) cc_final: 0.7775 (m-80) REVERT: C 286 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7509 (t-90) REVERT: C 524 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 581 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7959 (tpp80) REVERT: B 108 LYS cc_start: 0.7828 (tptt) cc_final: 0.7482 (tptt) REVERT: B 259 PHE cc_start: 0.8032 (m-80) cc_final: 0.7784 (m-80) REVERT: B 286 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7510 (t-90) REVERT: B 524 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 581 ARG cc_start: 0.8526 (ttp80) cc_final: 0.7966 (tpp80) REVERT: A 108 LYS cc_start: 0.7832 (tptt) cc_final: 0.7509 (tptt) REVERT: A 259 PHE cc_start: 0.8029 (m-80) cc_final: 0.7781 (m-80) REVERT: A 286 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7508 (t-90) REVERT: A 524 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8132 (p) REVERT: A 581 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7966 (tpp80) outliers start: 20 outliers final: 4 residues processed: 268 average time/residue: 0.2657 time to fit residues: 109.2423 Evaluate side-chains 244 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 211 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.173715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127646 restraints weight = 20267.979| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.13 r_work: 0.3431 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17396 Z= 0.157 Angle : 0.515 7.486 23560 Z= 0.263 Chirality : 0.040 0.178 2628 Planarity : 0.004 0.039 2956 Dihedral : 6.851 132.216 2372 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.98 % Allowed : 12.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2116 helix: 1.91 (0.14), residues: 1496 sheet: -0.10 (0.55), residues: 88 loop : -1.51 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 281 HIS 0.003 0.001 HIS B 421 PHE 0.010 0.001 PHE A 514 TYR 0.013 0.001 TYR D 411 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 1149) hydrogen bonds : angle 3.64502 ( 3363) covalent geometry : bond 0.00366 (17396) covalent geometry : angle 0.51456 (23560) *********************** 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 279 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.770 Fit side-chains REVERT: D 259 PHE cc_start: 0.8034 (m-80) cc_final: 0.7782 (m-80) REVERT: D 286 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: D 524 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8077 (p) REVERT: D 581 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7921 (tpp80) REVERT: C 259 PHE cc_start: 0.8031 (m-80) cc_final: 0.7778 (m-80) REVERT: C 286 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: C 524 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8082 (p) REVERT: C 581 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7919 (tpp80) REVERT: B 259 PHE cc_start: 0.8038 (m-80) cc_final: 0.7786 (m-80) REVERT: B 286 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: B 524 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 581 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7923 (tpp80) REVERT: A 259 PHE cc_start: 0.8038 (m-80) cc_final: 0.7786 (m-80) REVERT: A 286 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7542 (t-90) REVERT: A 524 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 581 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7928 (tpp80) outliers start: 35 outliers final: 12 residues processed: 260 average time/residue: 0.2538 time to fit residues: 102.6302 Evaluate side-chains 248 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 286 HIS 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 88 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 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 = 0.4082 r_free = 0.4082 target = 0.176125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128801 restraints weight = 20269.528| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.24 r_work: 0.3339 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17396 Z= 0.119 Angle : 0.489 7.452 23560 Z= 0.250 Chirality : 0.039 0.181 2628 Planarity : 0.003 0.038 2956 Dihedral : 6.844 132.599 2372 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.59 % Allowed : 12.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2116 helix: 2.04 (0.14), residues: 1492 sheet: -0.07 (0.55), residues: 88 loop : -1.41 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 133 HIS 0.003 0.001 HIS B 421 PHE 0.010 0.001 PHE D 514 TYR 0.013 0.001 TYR D 411 ARG 0.001 0.000 ARG D 467 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 1149) hydrogen bonds : angle 3.61022 ( 3363) covalent geometry : bond 0.00267 (17396) covalent geometry : angle 0.48929 (23560) *********************** 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 264 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 1.878 Fit side-chains REVERT: D 218 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8400 (mp) REVERT: D 259 PHE cc_start: 0.7950 (m-80) cc_final: 0.7705 (m-80) REVERT: D 286 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7535 (t-90) REVERT: D 454 ASN cc_start: 0.8420 (p0) cc_final: 0.8052 (p0) REVERT: D 523 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7636 (pt) REVERT: D 524 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.7956 (p) REVERT: D 581 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7929 (tpp80) REVERT: C 218 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8391 (mp) REVERT: C 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7703 (m-80) REVERT: C 286 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7531 (t-90) REVERT: C 454 ASN cc_start: 0.8417 (p0) cc_final: 0.8049 (p0) REVERT: C 523 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7626 (pt) REVERT: C 524 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.7949 (p) REVERT: C 581 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7930 (tpp80) REVERT: B 218 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 259 PHE cc_start: 0.7949 (m-80) cc_final: 0.7707 (m-80) REVERT: B 286 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7531 (t-90) REVERT: B 454 ASN cc_start: 0.8411 (p0) cc_final: 0.8040 (p0) REVERT: B 523 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7622 (pt) REVERT: B 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 581 ARG cc_start: 0.8516 (ttp80) cc_final: 0.7928 (tpp80) REVERT: A 218 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 259 PHE cc_start: 0.7949 (m-80) cc_final: 0.7708 (m-80) REVERT: A 286 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7535 (t-90) REVERT: A 454 ASN cc_start: 0.8420 (p0) cc_final: 0.8048 (p0) REVERT: A 523 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7635 (pt) REVERT: A 524 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 581 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7933 (tpp80) outliers start: 28 outliers final: 8 residues processed: 252 average time/residue: 0.2701 time to fit residues: 105.5757 Evaluate side-chains 252 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.168710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121180 restraints weight = 20315.000| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.18 r_work: 0.3305 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.005 0.033 17396 Z= 0.199 Angle : 0.541 7.754 23560 Z= 0.280 Chirality : 0.041 0.157 2628 Planarity : 0.004 0.046 2956 Dihedral : 6.836 131.542 2372 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.27 % Allowed : 12.64 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 2116 helix: 1.94 (0.14), residues: 1496 sheet: 0.10 (0.54), residues: 88 loop : -1.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 281 HIS 0.003 0.001 HIS B 392 PHE 0.011 0.001 PHE A 514 TYR 0.014 0.002 TYR B 411 ARG 0.002 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1149) hydrogen bonds : angle 3.68861 ( 3363) covalent geometry : bond 0.00479 (17396) covalent geometry : angle 0.54073 (23560) *********************** 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 271 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.760 Fit side-chains REVERT: D 218 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 259 PHE cc_start: 0.7919 (m-80) cc_final: 0.7678 (m-80) REVERT: D 286 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7557 (t-90) REVERT: D 523 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7618 (pt) REVERT: D 524 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8271 (t) REVERT: D 581 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8032 (tpp80) REVERT: C 218 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8519 (mp) REVERT: C 259 PHE cc_start: 0.7921 (m-80) cc_final: 0.7680 (m-80) REVERT: C 286 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7549 (t-90) REVERT: C 523 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7619 (pt) REVERT: C 524 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 581 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8025 (tpp80) REVERT: B 218 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 259 PHE cc_start: 0.7922 (m-80) cc_final: 0.7684 (m-80) REVERT: B 286 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7548 (t-90) REVERT: B 523 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7602 (pt) REVERT: B 524 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8263 (t) REVERT: B 581 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8026 (tpp80) REVERT: A 218 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 259 PHE cc_start: 0.7924 (m-80) cc_final: 0.7685 (m-80) REVERT: A 286 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7590 (t-90) REVERT: A 287 MET cc_start: 0.7445 (tpp) cc_final: 0.7198 (tpp) REVERT: A 523 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7604 (pt) REVERT: A 524 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (t) REVERT: A 581 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8027 (tpp80) outliers start: 40 outliers final: 15 residues processed: 259 average time/residue: 0.2764 time to fit residues: 109.2415 Evaluate side-chains 247 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.171098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123446 restraints weight = 20027.568| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.24 r_work: 0.3333 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1488 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 : 0.493 7.542 23560 Z= 0.250 Chirality : 0.039 0.204 2628 Planarity : 0.003 0.043 2956 Dihedral : 6.831 132.627 2372 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.59 % Allowed : 13.27 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2116 helix: 2.13 (0.14), residues: 1496 sheet: 0.07 (0.55), residues: 88 loop : -1.35 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.016 0.001 PHE B 236 TYR 0.013 0.001 TYR C 411 ARG 0.004 0.000 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 1149) hydrogen bonds : angle 3.55832 ( 3363) covalent geometry : bond 0.00258 (17396) covalent geometry : angle 0.49288 (23560) *********************** 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 275 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 2.016 Fit side-chains REVERT: D 218 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8357 (mp) REVERT: D 259 PHE cc_start: 0.7951 (m-80) cc_final: 0.7704 (m-80) REVERT: D 286 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7539 (t-90) REVERT: D 454 ASN cc_start: 0.8376 (p0) cc_final: 0.8043 (p0) REVERT: D 523 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7580 (pt) REVERT: D 524 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8258 (t) REVERT: D 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8049 (tpp80) REVERT: C 218 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 259 PHE cc_start: 0.7945 (m-80) cc_final: 0.7697 (m-80) REVERT: C 286 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7528 (t-90) REVERT: C 454 ASN cc_start: 0.8374 (p0) cc_final: 0.8042 (p0) REVERT: C 523 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7588 (pt) REVERT: C 524 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8263 (t) REVERT: C 581 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8048 (tpp80) REVERT: B 218 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8359 (mp) REVERT: B 259 PHE cc_start: 0.7959 (m-80) cc_final: 0.7715 (m-80) REVERT: B 286 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7531 (t-90) REVERT: B 454 ASN cc_start: 0.8352 (p0) cc_final: 0.8019 (p0) REVERT: B 523 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7585 (pt) REVERT: B 524 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (t) REVERT: B 581 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8052 (tpp80) REVERT: A 218 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 259 PHE cc_start: 0.7954 (m-80) cc_final: 0.7708 (m-80) REVERT: A 286 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7564 (t-90) REVERT: A 454 ASN cc_start: 0.8367 (p0) cc_final: 0.8036 (p0) REVERT: A 523 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7585 (pt) REVERT: A 524 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 581 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8051 (tpp80) outliers start: 28 outliers final: 12 residues processed: 267 average time/residue: 0.2483 time to fit residues: 104.4235 Evaluate side-chains 260 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.163791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116866 restraints weight = 20065.422| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.47 r_work: 0.3261 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17396 Z= 0.206 Angle : 0.549 7.766 23560 Z= 0.282 Chirality : 0.041 0.172 2628 Planarity : 0.004 0.051 2956 Dihedral : 6.836 131.674 2372 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.81 % Allowed : 14.34 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2116 helix: 2.01 (0.14), residues: 1496 sheet: 0.09 (0.54), residues: 88 loop : -1.41 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 281 HIS 0.003 0.001 HIS C 310 PHE 0.014 0.001 PHE B 236 TYR 0.015 0.002 TYR C 411 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1149) hydrogen bonds : angle 3.65630 ( 3363) covalent geometry : bond 0.00495 (17396) covalent geometry : angle 0.54903 (23560) *********************** 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 260 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.761 Fit side-chains REVERT: D 218 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8461 (mp) REVERT: D 259 PHE cc_start: 0.7916 (m-80) cc_final: 0.7689 (m-80) REVERT: D 286 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7648 (t-90) REVERT: D 523 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7511 (pt) REVERT: D 524 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8273 (t) REVERT: D 581 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8046 (tpp80) REVERT: C 218 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8452 (mp) REVERT: C 259 PHE cc_start: 0.7913 (m-80) cc_final: 0.7686 (m-80) REVERT: C 286 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: C 523 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7520 (pt) REVERT: C 524 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8277 (t) REVERT: C 581 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8055 (tpp80) REVERT: B 153 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7767 (mtt) REVERT: B 218 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 259 PHE cc_start: 0.7914 (m-80) cc_final: 0.7689 (m-80) REVERT: B 286 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7655 (t-90) REVERT: B 523 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7500 (pt) REVERT: B 524 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8271 (t) REVERT: B 581 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8054 (tpp80) REVERT: A 153 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: A 218 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 259 PHE cc_start: 0.7915 (m-80) cc_final: 0.7692 (m-80) REVERT: A 286 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7710 (t-90) REVERT: A 523 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7499 (pt) REVERT: A 524 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 581 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8051 (tpp80) outliers start: 32 outliers final: 12 residues processed: 248 average time/residue: 0.2505 time to fit residues: 96.8834 Evaluate side-chains 247 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 132 optimal weight: 0.0980 chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.167349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118989 restraints weight = 19790.037| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.28 r_work: 0.3331 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17396 Z= 0.114 Angle : 0.511 7.565 23560 Z= 0.255 Chirality : 0.039 0.172 2628 Planarity : 0.003 0.043 2956 Dihedral : 6.836 132.698 2372 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.15 % Allowed : 14.00 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2116 helix: 2.20 (0.14), residues: 1496 sheet: 0.08 (0.55), residues: 88 loop : -1.37 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.001 HIS A 421 PHE 0.018 0.001 PHE A 236 TYR 0.013 0.001 TYR C 411 ARG 0.004 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 1149) hydrogen bonds : angle 3.52753 ( 3363) covalent geometry : bond 0.00248 (17396) covalent geometry : angle 0.51143 (23560) *********************** 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 264 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.805 Fit side-chains REVERT: D 218 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 259 PHE cc_start: 0.7956 (m-80) cc_final: 0.7700 (m-80) REVERT: D 286 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7526 (t-90) REVERT: D 523 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7629 (pt) REVERT: D 524 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 218 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 259 PHE cc_start: 0.7939 (m-80) cc_final: 0.7685 (m-80) REVERT: C 286 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7521 (t-90) REVERT: C 523 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7638 (pt) REVERT: C 524 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8270 (t) REVERT: B 153 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: B 218 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8249 (mp) REVERT: B 259 PHE cc_start: 0.7963 (m-80) cc_final: 0.7711 (m-80) REVERT: B 286 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7528 (t-90) REVERT: B 523 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7619 (pt) REVERT: B 524 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (t) REVERT: A 112 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7350 (mtp180) REVERT: A 153 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: A 218 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 259 PHE cc_start: 0.7964 (m-80) cc_final: 0.7711 (m-80) REVERT: A 286 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7597 (t-90) REVERT: A 523 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7628 (pt) REVERT: A 524 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 581 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8095 (tpp80) outliers start: 38 outliers final: 12 residues processed: 254 average time/residue: 0.2338 time to fit residues: 96.7908 Evaluate side-chains 252 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.1744 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.167267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119712 restraints weight = 20171.711| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.18 r_work: 0.3287 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17396 Z= 0.226 Angle : 0.585 8.526 23560 Z= 0.301 Chirality : 0.042 0.219 2628 Planarity : 0.004 0.059 2956 Dihedral : 6.853 131.784 2372 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.10 % Allowed : 14.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.19), residues: 2116 helix: 2.01 (0.14), residues: 1488 sheet: 0.07 (0.55), residues: 88 loop : -1.43 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 373 HIS 0.003 0.001 HIS B 392 PHE 0.013 0.001 PHE D 514 TYR 0.016 0.002 TYR D 411 ARG 0.002 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1149) hydrogen bonds : angle 3.68145 ( 3363) covalent geometry : bond 0.00543 (17396) covalent geometry : angle 0.58534 (23560) *********************** 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 275 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 1.890 Fit side-chains REVERT: D 218 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 259 PHE cc_start: 0.7947 (m-80) cc_final: 0.7709 (m-80) REVERT: D 286 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7711 (t-90) REVERT: D 523 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7547 (pt) REVERT: D 524 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8285 (t) REVERT: D 581 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8093 (tpp80) REVERT: C 218 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 259 PHE cc_start: 0.7933 (m-80) cc_final: 0.7695 (m-80) REVERT: C 286 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: C 523 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7538 (pt) REVERT: C 524 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8277 (t) REVERT: C 581 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8093 (tpp80) REVERT: B 218 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7709 (m-80) REVERT: B 286 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: B 523 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7531 (pt) REVERT: B 524 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8272 (t) REVERT: B 581 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8091 (tpp80) REVERT: A 218 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7711 (m-80) REVERT: A 286 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: A 523 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7526 (pt) REVERT: A 524 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8091 (tpp80) outliers start: 37 outliers final: 16 residues processed: 265 average time/residue: 0.2467 time to fit residues: 104.5316 Evaluate side-chains 261 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 138 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.169535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121800 restraints weight = 20027.289| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.25 r_work: 0.3319 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1755 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= 0.126 Angle : 0.543 8.967 23560 Z= 0.272 Chirality : 0.040 0.212 2628 Planarity : 0.004 0.052 2956 Dihedral : 6.819 132.007 2372 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.81 % Allowed : 14.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2116 helix: 2.14 (0.14), residues: 1492 sheet: 0.04 (0.55), residues: 88 loop : -1.38 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.017 0.001 PHE A 236 TYR 0.013 0.001 TYR D 411 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 1149) hydrogen bonds : angle 3.58283 ( 3363) covalent geometry : bond 0.00286 (17396) covalent geometry : angle 0.54313 (23560) ********************** 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 269 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.758 Fit side-chains REVERT: D 218 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8244 (mp) REVERT: D 259 PHE cc_start: 0.7918 (m-80) cc_final: 0.7679 (m-80) REVERT: D 286 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7594 (t-90) REVERT: D 523 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7561 (pt) REVERT: D 524 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (t) REVERT: D 530 MET cc_start: 0.7866 (ptp) cc_final: 0.7571 (ptp) REVERT: D 581 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8150 (tpp80) REVERT: C 218 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 259 PHE cc_start: 0.7915 (m-80) cc_final: 0.7676 (m-80) REVERT: C 286 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: C 523 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7558 (pt) REVERT: C 524 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8264 (t) REVERT: C 530 MET cc_start: 0.7863 (ptp) cc_final: 0.7569 (ptp) REVERT: C 581 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8150 (tpp80) REVERT: B 218 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 259 PHE cc_start: 0.7925 (m-80) cc_final: 0.7686 (m-80) REVERT: B 286 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: B 523 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7545 (pt) REVERT: B 524 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 530 MET cc_start: 0.7829 (ptp) cc_final: 0.7537 (ptp) REVERT: B 581 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8147 (tpp80) REVERT: A 112 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7346 (mtp180) REVERT: A 218 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 259 PHE cc_start: 0.7924 (m-80) cc_final: 0.7689 (m-80) REVERT: A 286 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: A 454 ASN cc_start: 0.8378 (p0) cc_final: 0.8059 (p0) REVERT: A 523 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7535 (pt) REVERT: A 524 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8256 (t) REVERT: A 530 MET cc_start: 0.7818 (ptp) cc_final: 0.7521 (ptp) REVERT: A 581 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8153 (tpp80) outliers start: 32 outliers final: 16 residues processed: 261 average time/residue: 0.2499 time to fit residues: 104.3532 Evaluate side-chains 269 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.171625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124613 restraints weight = 19819.286| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.17 r_work: 0.3350 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17396 Z= 0.116 Angle : 0.516 7.643 23560 Z= 0.260 Chirality : 0.039 0.201 2628 Planarity : 0.004 0.049 2956 Dihedral : 6.802 132.400 2372 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.93 % Allowed : 14.29 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 2116 helix: 2.23 (0.14), residues: 1496 sheet: 0.05 (0.55), residues: 88 loop : -1.36 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.011 0.001 PHE A 514 TYR 0.012 0.001 TYR C 411 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 1149) hydrogen bonds : angle 3.49257 ( 3363) covalent geometry : bond 0.00258 (17396) covalent geometry : angle 0.51596 (23560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10090.67 seconds wall clock time: 174 minutes 43.00 seconds (10483.00 seconds total)