Starting phenix.real_space_refine on Sun Jun 15 05:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4m_41036/06_2025/8t4m_41036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4m_41036/06_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_41036/06_2025/8t4m_41036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4m_41036/06_2025/8t4m_41036.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4m_41036/06_2025/8t4m_41036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4m_41036/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.82, per 1000 atoms: 0.64 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: 5.28 Conformation dependent library (CDL) restraints added in 3.5 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: 2.20 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: 8.83 Time building geometry restraints manager: 6.05 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: 0.13 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.500 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.390 ------------------------------------------------------------------------------- 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 : 1.883 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: 0.3417 time to fit residues: 146.5895 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 : 1.595 ------------------------------------------------------------------------------- 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 = 0.173782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127331 restraints weight = 20297.736| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.14 r_work: 0.3425 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1024 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= 0.187 Angle : 0.550 7.748 23560 Z= 0.282 Chirality : 0.041 0.174 2628 Planarity : 0.004 0.039 2956 Dihedral : 6.826 131.676 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 0.03547 ( 1149) hydrogen bonds : angle 3.71690 ( 3363) covalent geometry : bond 0.00445 (17396) covalent geometry : angle 0.55000 (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 272 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 1.766 Fit side-chains REVERT: D 108 LYS cc_start: 0.7821 (tptt) cc_final: 0.7480 (tptt) REVERT: D 259 PHE cc_start: 0.8033 (m-80) cc_final: 0.7787 (m-80) REVERT: D 286 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: D 524 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8125 (p) REVERT: D 581 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7961 (tpp80) REVERT: C 108 LYS cc_start: 0.7826 (tptt) cc_final: 0.7478 (tptt) REVERT: C 259 PHE cc_start: 0.8030 (m-80) cc_final: 0.7786 (m-80) REVERT: C 286 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: C 524 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8116 (p) REVERT: C 581 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7958 (tpp80) REVERT: B 108 LYS cc_start: 0.7824 (tptt) cc_final: 0.7478 (tptt) REVERT: B 259 PHE cc_start: 0.8040 (m-80) cc_final: 0.7794 (m-80) REVERT: B 286 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (t-90) REVERT: B 524 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 581 ARG cc_start: 0.8532 (ttp80) cc_final: 0.7966 (tpp80) REVERT: A 108 LYS cc_start: 0.7830 (tptt) cc_final: 0.7506 (tptt) REVERT: A 259 PHE cc_start: 0.8037 (m-80) cc_final: 0.7793 (m-80) REVERT: A 286 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7515 (t-90) REVERT: A 524 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 581 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7966 (tpp80) outliers start: 20 outliers final: 4 residues processed: 264 average time/residue: 0.2746 time to fit residues: 111.6975 Evaluate side-chains 240 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 0.7980 chunk 203 optimal weight: 0.0770 chunk 201 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.169657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121641 restraints weight = 19828.049| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.30 r_work: 0.3366 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17396 Z= 0.103 Angle : 0.485 7.298 23560 Z= 0.243 Chirality : 0.038 0.186 2628 Planarity : 0.003 0.034 2956 Dihedral : 6.850 133.213 2372 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.64 % Allowed : 13.10 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.19), residues: 2116 helix: 2.03 (0.14), residues: 1500 sheet: 0.00 (0.55), residues: 88 loop : -1.39 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 133 HIS 0.002 0.001 HIS C 421 PHE 0.008 0.001 PHE A 514 TYR 0.011 0.001 TYR A 411 ARG 0.001 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 1149) hydrogen bonds : angle 3.54672 ( 3363) covalent geometry : bond 0.00214 (17396) covalent geometry : angle 0.48524 (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 297 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 2.040 Fit side-chains REVERT: D 259 PHE cc_start: 0.7920 (m-80) cc_final: 0.7666 (m-80) REVERT: D 286 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: D 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8052 (p) REVERT: D 581 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7967 (tpp80) REVERT: C 259 PHE cc_start: 0.7914 (m-80) cc_final: 0.7661 (m-80) REVERT: C 286 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7492 (t-90) REVERT: C 524 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8045 (p) REVERT: C 581 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7961 (tpp80) REVERT: B 259 PHE cc_start: 0.7927 (m-80) cc_final: 0.7674 (m-80) REVERT: B 286 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: B 524 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8049 (p) REVERT: B 581 ARG cc_start: 0.8519 (ttp80) cc_final: 0.7968 (tpp80) REVERT: A 259 PHE cc_start: 0.7930 (m-80) cc_final: 0.7679 (m-80) REVERT: A 286 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: A 524 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8049 (p) REVERT: A 581 ARG cc_start: 0.8529 (ttp80) cc_final: 0.7978 (tpp80) outliers start: 29 outliers final: 6 residues processed: 284 average time/residue: 0.2809 time to fit residues: 122.4886 Evaluate side-chains 266 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 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 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: 3.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.170769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122997 restraints weight = 19992.892| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.24 r_work: 0.3337 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.137 Angle : 0.494 7.493 23560 Z= 0.251 Chirality : 0.039 0.196 2628 Planarity : 0.003 0.047 2956 Dihedral : 6.798 132.446 2372 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 13.78 % Favored : 84.69 % 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: 2.13 (0.14), residues: 1500 sheet: -0.07 (0.55), residues: 88 loop : -1.38 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 281 HIS 0.003 0.001 HIS A 421 PHE 0.010 0.001 PHE A 514 TYR 0.012 0.001 TYR C 411 ARG 0.004 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 1149) hydrogen bonds : angle 3.49458 ( 3363) covalent geometry : bond 0.00316 (17396) covalent geometry : angle 0.49416 (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 263 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 1.772 Fit side-chains REVERT: D 113 MET cc_start: 0.8663 (mmm) cc_final: 0.8451 (mmm) REVERT: D 259 PHE cc_start: 0.7945 (m-80) cc_final: 0.7689 (m-80) REVERT: D 286 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7523 (t-90) REVERT: D 454 ASN cc_start: 0.8451 (p0) cc_final: 0.8048 (p0) REVERT: D 523 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7717 (pt) REVERT: D 524 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.7990 (p) REVERT: D 581 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7942 (tpp80) REVERT: C 113 MET cc_start: 0.8628 (mmm) cc_final: 0.8414 (mmm) REVERT: C 259 PHE cc_start: 0.7949 (m-80) cc_final: 0.7694 (m-80) REVERT: C 286 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: C 454 ASN cc_start: 0.8439 (p0) cc_final: 0.8035 (p0) REVERT: C 523 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7703 (pt) REVERT: C 524 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.7984 (p) REVERT: C 581 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7931 (tpp80) REVERT: B 113 MET cc_start: 0.8660 (mmm) cc_final: 0.8447 (mmm) REVERT: B 259 PHE cc_start: 0.7941 (m-80) cc_final: 0.7688 (m-80) REVERT: B 286 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: B 454 ASN cc_start: 0.8431 (p0) cc_final: 0.8025 (p0) REVERT: B 523 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7685 (pt) REVERT: B 524 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 581 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7931 (tpp80) REVERT: A 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7690 (m-80) REVERT: A 286 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7523 (t-90) REVERT: A 454 ASN cc_start: 0.8439 (p0) cc_final: 0.8033 (p0) REVERT: A 523 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7707 (pt) REVERT: A 524 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 581 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7938 (tpp80) outliers start: 27 outliers final: 11 residues processed: 251 average time/residue: 0.2600 time to fit residues: 102.5409 Evaluate side-chains 263 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 137 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 162 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN A 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127926 restraints weight = 20553.760| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.25 r_work: 0.3328 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17396 Z= 0.140 Angle : 0.491 7.532 23560 Z= 0.249 Chirality : 0.039 0.162 2628 Planarity : 0.003 0.043 2956 Dihedral : 6.787 132.251 2372 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.87 % Allowed : 13.15 % Favored : 84.98 % 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: 1.86 (0.19), residues: 2116 helix: 2.15 (0.14), residues: 1500 sheet: 0.04 (0.54), residues: 88 loop : -1.32 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE A 514 TYR 0.012 0.001 TYR D 411 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 1149) hydrogen bonds : angle 3.47932 ( 3363) covalent geometry : bond 0.00326 (17396) covalent geometry : angle 0.49145 (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 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 1.867 Fit side-chains REVERT: D 113 MET cc_start: 0.8725 (mmm) cc_final: 0.8508 (mmm) REVERT: D 218 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8333 (mp) REVERT: D 259 PHE cc_start: 0.7958 (m-80) cc_final: 0.7714 (m-80) REVERT: D 286 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7591 (t-90) REVERT: D 454 ASN cc_start: 0.8482 (p0) cc_final: 0.8090 (p0) REVERT: D 523 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7648 (pt) REVERT: D 524 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8263 (t) REVERT: D 581 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8047 (tpp80) REVERT: C 218 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 259 PHE cc_start: 0.7957 (m-80) cc_final: 0.7715 (m-80) REVERT: C 286 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: C 454 ASN cc_start: 0.8474 (p0) cc_final: 0.8084 (p0) REVERT: C 523 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7644 (pt) REVERT: C 524 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8265 (t) REVERT: C 581 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8049 (tpp80) REVERT: B 218 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 259 PHE cc_start: 0.7953 (m-80) cc_final: 0.7715 (m-80) REVERT: B 286 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7592 (t-90) REVERT: B 454 ASN cc_start: 0.8471 (p0) cc_final: 0.8077 (p0) REVERT: B 523 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7627 (pt) REVERT: B 524 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (t) REVERT: B 581 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8048 (tpp80) REVERT: A 218 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 259 PHE cc_start: 0.7960 (m-80) cc_final: 0.7718 (m-80) REVERT: A 286 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7557 (t-90) REVERT: A 454 ASN cc_start: 0.8470 (p0) cc_final: 0.8078 (p0) REVERT: A 523 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7628 (pt) REVERT: A 524 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8048 (tpp80) outliers start: 33 outliers final: 12 residues processed: 263 average time/residue: 0.2615 time to fit residues: 107.9761 Evaluate side-chains 261 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 184 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.176431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129879 restraints weight = 20235.252| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.23 r_work: 0.3358 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17396 Z= 0.109 Angle : 0.486 7.465 23560 Z= 0.244 Chirality : 0.038 0.157 2628 Planarity : 0.003 0.038 2956 Dihedral : 6.792 132.654 2372 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.93 % Allowed : 13.72 % Favored : 84.35 % 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: 1.98 (0.19), residues: 2116 helix: 2.25 (0.14), residues: 1496 sheet: -0.03 (0.55), residues: 88 loop : -1.25 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE C 514 TYR 0.011 0.001 TYR C 411 ARG 0.004 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 1149) hydrogen bonds : angle 3.41888 ( 3363) covalent geometry : bond 0.00237 (17396) covalent geometry : angle 0.48553 (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 263 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 2.687 Fit side-chains REVERT: D 218 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8214 (mp) REVERT: D 259 PHE cc_start: 0.7958 (m-80) cc_final: 0.7706 (m-80) REVERT: D 286 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: D 523 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7669 (pt) REVERT: D 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8258 (t) REVERT: D 581 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8073 (tpp80) REVERT: C 218 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 259 PHE cc_start: 0.7955 (m-80) cc_final: 0.7703 (m-80) REVERT: C 286 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7452 (t-90) REVERT: C 287 MET cc_start: 0.7576 (tpp) cc_final: 0.7313 (tpt) REVERT: C 523 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7667 (pt) REVERT: C 524 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8252 (t) REVERT: C 581 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8073 (tpp80) REVERT: B 218 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 259 PHE cc_start: 0.7941 (m-80) cc_final: 0.7692 (m-80) REVERT: B 286 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7459 (t-90) REVERT: B 287 MET cc_start: 0.7580 (tpp) cc_final: 0.7319 (tpt) REVERT: B 523 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7648 (pt) REVERT: B 524 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8249 (t) REVERT: B 581 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8073 (tpp80) REVERT: A 113 MET cc_start: 0.8556 (mmm) cc_final: 0.8323 (mmm) REVERT: A 218 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 259 PHE cc_start: 0.7954 (m-80) cc_final: 0.7702 (m-80) REVERT: A 286 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7526 (t-90) REVERT: A 523 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7660 (pt) REVERT: A 524 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8260 (t) REVERT: A 581 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8077 (tpp80) outliers start: 34 outliers final: 12 residues processed: 249 average time/residue: 0.3410 time to fit residues: 132.6703 Evaluate side-chains 254 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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: 3.9990 chunk 123 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.175427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128540 restraints weight = 20289.758| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3338 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.129 Angle : 0.490 7.549 23560 Z= 0.247 Chirality : 0.039 0.149 2628 Planarity : 0.003 0.041 2956 Dihedral : 6.782 132.475 2372 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 13.83 % Favored : 84.24 % 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: 1.95 (0.19), residues: 2116 helix: 2.23 (0.14), residues: 1496 sheet: 0.04 (0.54), residues: 88 loop : -1.29 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.003 0.001 HIS A 421 PHE 0.010 0.001 PHE D 514 TYR 0.011 0.001 TYR C 411 ARG 0.002 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 1149) hydrogen bonds : angle 3.46196 ( 3363) covalent geometry : bond 0.00296 (17396) covalent geometry : angle 0.49013 (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 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 2.379 Fit side-chains REVERT: D 218 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 259 PHE cc_start: 0.7969 (m-80) cc_final: 0.7713 (m-80) REVERT: D 286 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: D 454 ASN cc_start: 0.8415 (p0) cc_final: 0.8066 (p0) REVERT: D 523 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7741 (pt) REVERT: D 524 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8268 (t) REVERT: D 581 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8086 (tpp80) REVERT: C 218 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 259 PHE cc_start: 0.7963 (m-80) cc_final: 0.7709 (m-80) REVERT: C 286 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7530 (t-90) REVERT: C 454 ASN cc_start: 0.8404 (p0) cc_final: 0.8055 (p0) REVERT: C 523 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7756 (pt) REVERT: C 524 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8266 (t) REVERT: C 581 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8085 (tpp80) REVERT: B 218 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 259 PHE cc_start: 0.7957 (m-80) cc_final: 0.7706 (m-80) REVERT: B 286 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7537 (t-90) REVERT: B 454 ASN cc_start: 0.8397 (p0) cc_final: 0.8050 (p0) REVERT: B 523 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7734 (pt) REVERT: B 524 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 581 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8087 (tpp80) REVERT: A 113 MET cc_start: 0.8695 (mmm) cc_final: 0.8433 (mmm) REVERT: A 218 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 259 PHE cc_start: 0.7960 (m-80) cc_final: 0.7709 (m-80) REVERT: A 286 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7538 (t-90) REVERT: A 454 ASN cc_start: 0.8403 (p0) cc_final: 0.8053 (p0) REVERT: A 523 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7739 (pt) REVERT: A 524 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 581 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8092 (tpp80) outliers start: 34 outliers final: 12 residues processed: 264 average time/residue: 0.3235 time to fit residues: 136.7309 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 : 2.258 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 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 = 0.4085 r_free = 0.4085 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128914 restraints weight = 20226.701| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.24 r_work: 0.3346 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17396 Z= 0.121 Angle : 0.503 8.034 23560 Z= 0.250 Chirality : 0.039 0.148 2628 Planarity : 0.003 0.039 2956 Dihedral : 6.783 132.815 2372 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.04 % Allowed : 14.17 % 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: 2.02 (0.19), residues: 2116 helix: 2.27 (0.14), residues: 1496 sheet: 0.03 (0.55), residues: 88 loop : -1.24 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 281 HIS 0.003 0.001 HIS B 421 PHE 0.010 0.001 PHE D 514 TYR 0.011 0.001 TYR B 411 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 1149) hydrogen bonds : angle 3.45168 ( 3363) covalent geometry : bond 0.00276 (17396) covalent geometry : angle 0.50339 (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 269 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 2.136 Fit side-chains REVERT: D 218 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 259 PHE cc_start: 0.7966 (m-80) cc_final: 0.7704 (m-80) REVERT: D 454 ASN cc_start: 0.8374 (p0) cc_final: 0.8041 (p0) REVERT: D 523 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7752 (pt) REVERT: D 524 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8275 (t) REVERT: D 581 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8076 (tpp80) REVERT: C 218 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 259 PHE cc_start: 0.7954 (m-80) cc_final: 0.7695 (m-80) REVERT: C 286 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7523 (t-90) REVERT: C 454 ASN cc_start: 0.8364 (p0) cc_final: 0.8033 (p0) REVERT: C 523 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7760 (pt) REVERT: C 524 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8275 (t) REVERT: C 581 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8082 (tpp80) REVERT: B 218 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 259 PHE cc_start: 0.7953 (m-80) cc_final: 0.7698 (m-80) REVERT: B 286 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: B 454 ASN cc_start: 0.8359 (p0) cc_final: 0.8028 (p0) REVERT: B 523 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7733 (pt) REVERT: B 524 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8266 (t) REVERT: B 581 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8075 (tpp80) REVERT: A 113 MET cc_start: 0.8613 (mmm) cc_final: 0.8361 (mmm) REVERT: A 218 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 259 PHE cc_start: 0.7959 (m-80) cc_final: 0.7702 (m-80) REVERT: A 286 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7586 (t-90) REVERT: A 454 ASN cc_start: 0.8363 (p0) cc_final: 0.8029 (p0) REVERT: A 523 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7747 (pt) REVERT: A 524 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (t) REVERT: A 581 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8083 (tpp80) outliers start: 36 outliers final: 12 residues processed: 257 average time/residue: 0.2679 time to fit residues: 108.7227 Evaluate side-chains 260 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 170 optimal weight: 0.0000 chunk 135 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 overall best weight: 0.5504 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130967 restraints weight = 20247.202| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.22 r_work: 0.3367 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17396 Z= 0.107 Angle : 0.503 7.689 23560 Z= 0.252 Chirality : 0.038 0.147 2628 Planarity : 0.003 0.037 2956 Dihedral : 6.758 132.896 2372 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.87 % Allowed : 14.12 % Favored : 84.01 % 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: 2.07 (0.19), residues: 2116 helix: 2.32 (0.14), residues: 1500 sheet: 0.02 (0.55), residues: 88 loop : -1.25 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE B 514 TYR 0.010 0.001 TYR C 411 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 1149) hydrogen bonds : angle 3.39806 ( 3363) covalent geometry : bond 0.00231 (17396) covalent geometry : angle 0.50262 (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 266 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 2.044 Fit side-chains REVERT: D 218 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8304 (mp) REVERT: D 259 PHE cc_start: 0.7938 (m-80) cc_final: 0.7677 (m-80) REVERT: D 523 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7766 (pt) REVERT: D 524 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8272 (t) REVERT: C 218 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 259 PHE cc_start: 0.7929 (m-80) cc_final: 0.7671 (m-80) REVERT: C 286 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: C 523 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7757 (pt) REVERT: C 524 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8262 (t) REVERT: B 218 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 259 PHE cc_start: 0.7927 (m-80) cc_final: 0.7673 (m-80) REVERT: B 286 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7523 (t-90) REVERT: B 523 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7756 (pt) REVERT: B 524 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 113 MET cc_start: 0.8577 (mmm) cc_final: 0.8332 (mmm) REVERT: A 218 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 259 PHE cc_start: 0.7937 (m-80) cc_final: 0.7688 (m-80) REVERT: A 286 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: A 523 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7749 (pt) REVERT: A 524 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8269 (t) outliers start: 33 outliers final: 12 residues processed: 257 average time/residue: 0.2626 time to fit residues: 110.1322 Evaluate side-chains 257 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 138 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 167 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 126 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126605 restraints weight = 19933.688| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.24 r_work: 0.3380 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1605 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= 0.101 Angle : 0.507 7.687 23560 Z= 0.252 Chirality : 0.038 0.146 2628 Planarity : 0.003 0.036 2956 Dihedral : 6.757 133.199 2372 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.53 % Allowed : 14.34 % Favored : 84.13 % 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: 2.18 (0.19), residues: 2116 helix: 2.39 (0.14), residues: 1500 sheet: 0.06 (0.55), residues: 88 loop : -1.22 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 281 HIS 0.003 0.001 HIS C 421 PHE 0.019 0.001 PHE A 236 TYR 0.009 0.001 TYR C 411 ARG 0.002 0.000 ARG C 195 Details of bonding type rmsd hydrogen bonds : bond 0.02670 ( 1149) hydrogen bonds : angle 3.35187 ( 3363) covalent geometry : bond 0.00212 (17396) covalent geometry : angle 0.50705 (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 267 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 1.730 Fit side-chains REVERT: D 218 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 259 PHE cc_start: 0.7941 (m-80) cc_final: 0.7671 (m-80) REVERT: D 523 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7804 (pt) REVERT: D 524 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 218 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7659 (m-80) REVERT: C 286 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7500 (t-90) REVERT: C 523 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (pt) REVERT: C 524 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 218 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7665 (m-80) REVERT: B 286 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7509 (t-90) REVERT: B 523 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7797 (pt) REVERT: B 524 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 113 MET cc_start: 0.8587 (mmm) cc_final: 0.8215 (tpt) REVERT: A 218 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 259 PHE cc_start: 0.7949 (m-80) cc_final: 0.7684 (m-80) REVERT: A 286 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7535 (t-90) REVERT: A 523 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (pt) REVERT: A 524 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.7971 (p) outliers start: 27 outliers final: 11 residues processed: 260 average time/residue: 0.2384 time to fit residues: 100.2445 Evaluate side-chains 263 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 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 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: 2.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121127 restraints weight = 20027.742| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.24 r_work: 0.3313 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17396 Z= 0.177 Angle : 0.557 7.913 23560 Z= 0.280 Chirality : 0.040 0.142 2628 Planarity : 0.003 0.045 2956 Dihedral : 6.769 131.902 2372 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.76 % Allowed : 14.29 % Favored : 83.96 % 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: 1.96 (0.19), residues: 2116 helix: 2.20 (0.14), residues: 1504 sheet: 0.18 (0.54), residues: 88 loop : -1.26 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 281 HIS 0.002 0.001 HIS A 392 PHE 0.022 0.001 PHE A 236 TYR 0.013 0.001 TYR A 411 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 1149) hydrogen bonds : angle 3.50462 ( 3363) covalent geometry : bond 0.00421 (17396) covalent geometry : angle 0.55669 (23560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10535.20 seconds wall clock time: 186 minutes 46.76 seconds (11206.76 seconds total)