Starting phenix.real_space_refine on Thu Mar 5 06:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8a_20686/03_2026/6u8a_20686.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.23 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 859.5 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 61.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.619A pdb=" N THR C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.037A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.837A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.623A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.661A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.659A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 26945 2.34 - 4.67: 796 4.67 - 7.01: 83 7.01 - 9.34: 36 9.34 - 11.68: 16 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10837 19.27 - 38.53: 1023 38.53 - 57.80: 196 57.80 - 77.07: 32 77.07 - 96.33: 12 Dihedral angle restraints: 12100 sinusoidal: 4880 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6104 2.82 - 3.34: 17959 3.34 - 3.86: 33559 3.86 - 4.38: 37894 4.38 - 4.90: 66133 Nonbonded interactions: 161649 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 3.040 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 3.120 ... (remaining 161644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.008 0.065 20544 Z= 0.343 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.898 96.335 7428 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 392 TYR 0.013 0.002 TYR D 111 PHE 0.019 0.003 PHE B 161 TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00806 (20544) covalent geometry : angle 0.96569 (27876) hydrogen bonds : bond 0.14053 ( 1072) hydrogen bonds : angle 6.14329 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7254 (mm) cc_final: 0.6675 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8199 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7901 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8904 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7601 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7060 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7436 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5830 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7087 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5859 (m100) REVERT: D 473 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7528 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7568 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7189 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.1380 time to fit residues: 87.9646 Evaluate side-chains 271 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 316 GLN B 163 GLN B 186 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 316 GLN C 186 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 316 GLN D 186 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 316 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129015 restraints weight = 26943.600| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.79 r_work: 0.3323 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20544 Z= 0.099 Angle : 0.508 7.622 27876 Z= 0.259 Chirality : 0.036 0.192 3148 Planarity : 0.005 0.063 3420 Dihedral : 6.767 54.909 2772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.09 % Allowed : 13.04 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.16), residues: 2428 helix: 0.06 (0.13), residues: 1452 sheet: -2.16 (0.47), residues: 92 loop : -1.84 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.015 0.001 TYR D 455 PHE 0.017 0.001 PHE C 467 TRP 0.014 0.001 TRP A 715 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00210 (20544) covalent geometry : angle 0.50760 (27876) hydrogen bonds : bond 0.03327 ( 1072) hydrogen bonds : angle 4.06329 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 381 time to evaluate : 0.868 Fit side-chains REVERT: A 92 LEU cc_start: 0.7326 (mm) cc_final: 0.6427 (pp) REVERT: A 178 GLN cc_start: 0.7853 (mt0) cc_final: 0.7441 (mp10) REVERT: A 454 TRP cc_start: 0.8133 (t-100) cc_final: 0.7843 (t60) REVERT: B 305 GLU cc_start: 0.8163 (tt0) cc_final: 0.7854 (mt-10) REVERT: B 318 GLU cc_start: 0.7277 (tt0) cc_final: 0.7009 (tt0) REVERT: B 324 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 372 MET cc_start: 0.9117 (mtt) cc_final: 0.8908 (mtt) REVERT: B 383 GLN cc_start: 0.8352 (tp40) cc_final: 0.8130 (tp40) REVERT: B 455 TYR cc_start: 0.9136 (t80) cc_final: 0.8867 (t80) REVERT: B 645 MET cc_start: 0.8254 (tmm) cc_final: 0.7812 (tmm) REVERT: B 687 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7600 (mtm110) REVERT: C 111 TYR cc_start: 0.6011 (m-80) cc_final: 0.5593 (m-80) REVERT: C 113 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 118 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8114 (tttt) REVERT: C 235 GLN cc_start: 0.7707 (mt0) cc_final: 0.7496 (mt0) REVERT: C 305 GLU cc_start: 0.8239 (tt0) cc_final: 0.7915 (mt-10) REVERT: C 454 TRP cc_start: 0.8213 (t-100) cc_final: 0.7944 (t60) REVERT: C 455 TYR cc_start: 0.9223 (t80) cc_final: 0.8983 (t80) REVERT: C 457 TRP cc_start: 0.8273 (t-100) cc_final: 0.8055 (t-100) REVERT: C 473 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8076 (mp0) REVERT: D 111 TYR cc_start: 0.6156 (m-80) cc_final: 0.5795 (m-80) REVERT: D 113 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7261 (mt-10) REVERT: D 118 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8008 (tttt) REVERT: D 235 GLN cc_start: 0.7712 (mt0) cc_final: 0.7478 (mt0) REVERT: D 255 MET cc_start: 0.8814 (mmm) cc_final: 0.8434 (mmt) REVERT: D 305 GLU cc_start: 0.8040 (tt0) cc_final: 0.7533 (mt-10) REVERT: D 358 GLU cc_start: 0.8225 (tt0) cc_final: 0.7804 (tt0) REVERT: D 454 TRP cc_start: 0.8108 (t-100) cc_final: 0.7883 (t60) outliers start: 45 outliers final: 19 residues processed: 408 average time/residue: 0.1296 time to fit residues: 85.2725 Evaluate side-chains 318 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 299 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 234 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 487 GLN B 414 GLN B 487 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 487 GLN D 163 GLN D 414 GLN D 487 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126569 restraints weight = 26978.113| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.80 r_work: 0.3300 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20544 Z= 0.099 Angle : 0.514 9.826 27876 Z= 0.250 Chirality : 0.036 0.196 3148 Planarity : 0.004 0.058 3420 Dihedral : 6.318 54.483 2772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.44 % Allowed : 16.11 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2428 helix: 1.00 (0.13), residues: 1472 sheet: -1.81 (0.49), residues: 92 loop : -1.68 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 317 TYR 0.012 0.001 TYR D 455 PHE 0.018 0.001 PHE D 467 TRP 0.008 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00220 (20544) covalent geometry : angle 0.51400 (27876) hydrogen bonds : bond 0.03083 ( 1072) hydrogen bonds : angle 3.78465 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7328 (mm) cc_final: 0.6348 (pp) REVERT: A 178 GLN cc_start: 0.7890 (mt0) cc_final: 0.7522 (mp10) REVERT: A 269 HIS cc_start: 0.7930 (t70) cc_final: 0.7546 (t70) REVERT: A 454 TRP cc_start: 0.8163 (t-100) cc_final: 0.7836 (t60) REVERT: A 647 GLU cc_start: 0.8964 (tt0) cc_final: 0.8622 (mt-10) REVERT: A 670 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7582 (tp30) REVERT: B 305 GLU cc_start: 0.8100 (tt0) cc_final: 0.7720 (mt-10) REVERT: B 324 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 383 GLN cc_start: 0.8384 (tp40) cc_final: 0.8162 (tp40) REVERT: B 455 TYR cc_start: 0.9175 (t80) cc_final: 0.8883 (t80) REVERT: B 645 MET cc_start: 0.8353 (tmm) cc_final: 0.7687 (tmm) REVERT: B 687 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7720 (mtm110) REVERT: C 111 TYR cc_start: 0.5857 (m-80) cc_final: 0.5460 (m-80) REVERT: C 113 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7096 (mt-10) REVERT: C 118 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8170 (ttpt) REVERT: C 178 GLN cc_start: 0.7890 (mt0) cc_final: 0.7508 (mp10) REVERT: C 235 GLN cc_start: 0.7753 (mt0) cc_final: 0.7536 (mt0) REVERT: C 305 GLU cc_start: 0.8166 (tt0) cc_final: 0.7805 (mt-10) REVERT: C 454 TRP cc_start: 0.8223 (t-100) cc_final: 0.7916 (t60) REVERT: C 455 TYR cc_start: 0.9196 (t80) cc_final: 0.8910 (t80) REVERT: C 470 SER cc_start: 0.8342 (t) cc_final: 0.7747 (t) REVERT: C 473 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8065 (mp0) REVERT: D 111 TYR cc_start: 0.5918 (m-80) cc_final: 0.5587 (m-80) REVERT: D 113 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7199 (mt-10) REVERT: D 118 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8028 (tttt) REVERT: D 178 GLN cc_start: 0.7915 (mt0) cc_final: 0.7534 (mp10) REVERT: D 235 GLN cc_start: 0.7742 (mt0) cc_final: 0.7513 (mt0) REVERT: D 269 HIS cc_start: 0.7862 (t70) cc_final: 0.7583 (t70) REVERT: D 454 TRP cc_start: 0.8133 (t-100) cc_final: 0.7903 (t60) REVERT: D 457 TRP cc_start: 0.8256 (t-100) cc_final: 0.7989 (t-100) outliers start: 31 outliers final: 17 residues processed: 348 average time/residue: 0.1244 time to fit residues: 69.6431 Evaluate side-chains 304 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 287 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.0060 chunk 159 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 125 optimal weight: 0.0870 chunk 223 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126271 restraints weight = 26969.754| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.80 r_work: 0.3292 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20544 Z= 0.103 Angle : 0.494 6.652 27876 Z= 0.245 Chirality : 0.036 0.169 3148 Planarity : 0.003 0.054 3420 Dihedral : 6.091 54.129 2772 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.42 % Allowed : 16.57 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2428 helix: 1.49 (0.14), residues: 1476 sheet: -1.58 (0.49), residues: 92 loop : -1.44 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 706 TYR 0.013 0.001 TYR D 455 PHE 0.019 0.001 PHE A 467 TRP 0.011 0.001 TRP B 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00233 (20544) covalent geometry : angle 0.49395 (27876) hydrogen bonds : bond 0.03010 ( 1072) hydrogen bonds : angle 3.63689 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7106 (mm) cc_final: 0.6212 (pp) REVERT: A 178 GLN cc_start: 0.7920 (mt0) cc_final: 0.7552 (mp10) REVERT: A 269 HIS cc_start: 0.8044 (t70) cc_final: 0.7695 (t70) REVERT: A 454 TRP cc_start: 0.8215 (t-100) cc_final: 0.7890 (t60) REVERT: A 647 GLU cc_start: 0.8937 (tt0) cc_final: 0.8473 (mt-10) REVERT: A 670 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7571 (tp30) REVERT: B 305 GLU cc_start: 0.8100 (tt0) cc_final: 0.7711 (mt-10) REVERT: B 383 GLN cc_start: 0.8339 (tp40) cc_final: 0.7856 (tt0) REVERT: B 634 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: B 645 MET cc_start: 0.8347 (tmm) cc_final: 0.7578 (tmm) REVERT: C 111 TYR cc_start: 0.5518 (m-80) cc_final: 0.5318 (m-80) REVERT: C 113 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6914 (mt-10) REVERT: C 118 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7995 (ttpt) REVERT: C 178 GLN cc_start: 0.8009 (mt0) cc_final: 0.7597 (mp10) REVERT: C 235 GLN cc_start: 0.7741 (mt0) cc_final: 0.7539 (mt0) REVERT: C 305 GLU cc_start: 0.8113 (tt0) cc_final: 0.7717 (mt-10) REVERT: C 454 TRP cc_start: 0.8271 (t-100) cc_final: 0.7946 (t60) REVERT: C 455 TYR cc_start: 0.9192 (t80) cc_final: 0.8939 (t80) REVERT: D 111 TYR cc_start: 0.5756 (m-80) cc_final: 0.5413 (m-80) REVERT: D 113 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7008 (mt-10) REVERT: D 178 GLN cc_start: 0.8120 (mt0) cc_final: 0.7662 (mp10) REVERT: D 224 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (p0) REVERT: D 235 GLN cc_start: 0.7801 (mt0) cc_final: 0.7552 (mt0) REVERT: D 454 TRP cc_start: 0.8179 (t-100) cc_final: 0.7920 (t60) REVERT: D 528 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8200 (ptp) REVERT: D 670 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7646 (tp30) outliers start: 52 outliers final: 21 residues processed: 352 average time/residue: 0.1251 time to fit residues: 70.9578 Evaluate side-chains 303 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 195 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 232 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 127 ASN B 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123597 restraints weight = 26917.628| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.80 r_work: 0.3265 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20544 Z= 0.122 Angle : 0.514 9.199 27876 Z= 0.253 Chirality : 0.037 0.166 3148 Planarity : 0.003 0.049 3420 Dihedral : 6.184 55.534 2772 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.65 % Allowed : 17.41 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2428 helix: 1.68 (0.14), residues: 1480 sheet: -1.54 (0.50), residues: 92 loop : -1.34 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 591 TYR 0.013 0.001 TYR B 455 PHE 0.020 0.001 PHE D 467 TRP 0.011 0.001 TRP A 715 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00284 (20544) covalent geometry : angle 0.51443 (27876) hydrogen bonds : bond 0.03116 ( 1072) hydrogen bonds : angle 3.66025 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.5964 (p90) REVERT: A 92 LEU cc_start: 0.7038 (mm) cc_final: 0.6156 (pp) REVERT: A 178 GLN cc_start: 0.8098 (mt0) cc_final: 0.7698 (mp10) REVERT: A 647 GLU cc_start: 0.8958 (tt0) cc_final: 0.8495 (mt-10) REVERT: B 39 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5586 (p90) REVERT: B 269 HIS cc_start: 0.8059 (t70) cc_final: 0.7716 (t70) REVERT: B 383 GLN cc_start: 0.8328 (tp40) cc_final: 0.7951 (tt0) REVERT: B 634 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: B 645 MET cc_start: 0.8484 (tmm) cc_final: 0.7707 (tmm) REVERT: C 39 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5573 (p90) REVERT: C 178 GLN cc_start: 0.8074 (mt0) cc_final: 0.7681 (mp10) REVERT: C 235 GLN cc_start: 0.7827 (mt0) cc_final: 0.7584 (mt0) REVERT: C 305 GLU cc_start: 0.8065 (tt0) cc_final: 0.7865 (mt-10) REVERT: C 455 TYR cc_start: 0.9189 (t80) cc_final: 0.8923 (t80) REVERT: C 670 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: D 111 TYR cc_start: 0.5606 (m-80) cc_final: 0.5230 (m-80) REVERT: D 178 GLN cc_start: 0.8052 (mt0) cc_final: 0.7626 (mp10) REVERT: D 670 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7658 (tp30) outliers start: 57 outliers final: 30 residues processed: 339 average time/residue: 0.1406 time to fit residues: 75.8638 Evaluate side-chains 305 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 185 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127247 restraints weight = 27005.068| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.93 r_work: 0.3279 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20544 Z= 0.102 Angle : 0.499 7.667 27876 Z= 0.245 Chirality : 0.036 0.255 3148 Planarity : 0.003 0.048 3420 Dihedral : 5.975 55.798 2772 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.47 % Allowed : 18.16 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2428 helix: 1.93 (0.14), residues: 1456 sheet: -2.40 (0.45), residues: 112 loop : -1.20 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 100 TYR 0.013 0.001 TYR A 455 PHE 0.021 0.001 PHE A 467 TRP 0.015 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00238 (20544) covalent geometry : angle 0.49919 (27876) hydrogen bonds : bond 0.02994 ( 1072) hydrogen bonds : angle 3.57897 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7030 (mm) cc_final: 0.6144 (pp) REVERT: A 178 GLN cc_start: 0.8048 (mt0) cc_final: 0.7672 (mp10) REVERT: A 647 GLU cc_start: 0.8952 (tt0) cc_final: 0.8467 (mt-10) REVERT: B 39 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.5620 (p90) REVERT: B 383 GLN cc_start: 0.8311 (tp40) cc_final: 0.7947 (tt0) REVERT: B 473 GLU cc_start: 0.8465 (mp0) cc_final: 0.8235 (mm-30) REVERT: B 634 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: B 645 MET cc_start: 0.8384 (tmm) cc_final: 0.8144 (ttm) REVERT: C 235 GLN cc_start: 0.7772 (mt0) cc_final: 0.7548 (mt0) REVERT: C 455 TYR cc_start: 0.9177 (t80) cc_final: 0.8906 (t80) REVERT: C 473 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 528 MET cc_start: 0.8511 (ptm) cc_final: 0.8199 (ttp) REVERT: D 39 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.5645 (p90) REVERT: D 92 LEU cc_start: 0.7730 (mt) cc_final: 0.6233 (pp) REVERT: D 111 TYR cc_start: 0.5492 (m-80) cc_final: 0.5158 (m-80) REVERT: D 178 GLN cc_start: 0.8054 (mt0) cc_final: 0.7643 (mp10) REVERT: D 255 MET cc_start: 0.8540 (mmt) cc_final: 0.8257 (mmm) REVERT: D 670 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7609 (tp30) outliers start: 53 outliers final: 34 residues processed: 333 average time/residue: 0.1230 time to fit residues: 66.1666 Evaluate side-chains 305 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS C 127 ASN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124353 restraints weight = 27388.397| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.75 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20544 Z= 0.193 Angle : 0.599 12.567 27876 Z= 0.287 Chirality : 0.039 0.175 3148 Planarity : 0.004 0.045 3420 Dihedral : 6.654 58.441 2772 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.70 % Allowed : 18.39 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2428 helix: 1.80 (0.14), residues: 1452 sheet: -1.61 (0.50), residues: 92 loop : -1.36 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.012 0.002 TYR B 455 PHE 0.021 0.002 PHE D 405 TRP 0.017 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00465 (20544) covalent geometry : angle 0.59923 (27876) hydrogen bonds : bond 0.03475 ( 1072) hydrogen bonds : angle 3.79063 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5760 (p90) REVERT: A 92 LEU cc_start: 0.7517 (mm) cc_final: 0.6559 (pp) REVERT: A 473 GLU cc_start: 0.8482 (mp0) cc_final: 0.8250 (mm-30) REVERT: A 528 MET cc_start: 0.8587 (ptm) cc_final: 0.8305 (ttp) REVERT: A 670 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: B 39 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6007 (p90) REVERT: B 383 GLN cc_start: 0.8402 (tp40) cc_final: 0.8101 (tt0) REVERT: B 473 GLU cc_start: 0.8519 (mp0) cc_final: 0.8295 (mm-30) REVERT: B 645 MET cc_start: 0.8620 (tmm) cc_final: 0.7779 (tmm) REVERT: C 39 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.5725 (p90) REVERT: C 455 TYR cc_start: 0.9239 (t80) cc_final: 0.8939 (t80) REVERT: C 528 MET cc_start: 0.8548 (ptm) cc_final: 0.8238 (ttp) REVERT: C 670 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: D 39 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5531 (p90) REVERT: D 92 LEU cc_start: 0.7752 (mt) cc_final: 0.6305 (pp) REVERT: D 670 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7720 (tp30) outliers start: 58 outliers final: 37 residues processed: 319 average time/residue: 0.1304 time to fit residues: 66.1960 Evaluate side-chains 302 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 115 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124843 restraints weight = 27161.966| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.84 r_work: 0.3278 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20544 Z= 0.103 Angle : 0.527 9.862 27876 Z= 0.254 Chirality : 0.036 0.163 3148 Planarity : 0.003 0.047 3420 Dihedral : 6.029 58.257 2772 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.19 % Allowed : 19.18 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2428 helix: 2.05 (0.14), residues: 1444 sheet: -1.63 (0.49), residues: 92 loop : -1.20 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.015 0.001 TYR D 455 PHE 0.023 0.001 PHE B 467 TRP 0.026 0.001 TRP D 715 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00237 (20544) covalent geometry : angle 0.52724 (27876) hydrogen bonds : bond 0.03008 ( 1072) hydrogen bonds : angle 3.60093 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.5742 (p90) REVERT: A 92 LEU cc_start: 0.7148 (mm) cc_final: 0.6288 (pp) REVERT: A 528 MET cc_start: 0.8502 (ptm) cc_final: 0.8264 (ttp) REVERT: A 647 GLU cc_start: 0.8875 (tt0) cc_final: 0.8284 (mt-10) REVERT: B 39 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5781 (p90) REVERT: B 92 LEU cc_start: 0.7486 (mt) cc_final: 0.6194 (pp) REVERT: B 305 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7885 (tt0) REVERT: B 383 GLN cc_start: 0.8319 (tp40) cc_final: 0.7968 (tt0) REVERT: B 473 GLU cc_start: 0.8434 (mp0) cc_final: 0.8216 (mm-30) REVERT: B 645 MET cc_start: 0.8587 (tmm) cc_final: 0.8185 (ttm) REVERT: C 39 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.5600 (p90) REVERT: C 92 LEU cc_start: 0.7636 (mt) cc_final: 0.6281 (pp) REVERT: C 235 GLN cc_start: 0.7866 (mt0) cc_final: 0.7633 (mt0) REVERT: C 305 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7912 (tt0) REVERT: C 455 TYR cc_start: 0.9178 (t80) cc_final: 0.8842 (t80) REVERT: C 528 MET cc_start: 0.8460 (ptm) cc_final: 0.8200 (ttp) REVERT: C 634 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: C 645 MET cc_start: 0.8532 (tmm) cc_final: 0.8226 (tmm) REVERT: C 670 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: D 39 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5567 (p90) REVERT: D 92 LEU cc_start: 0.7729 (mt) cc_final: 0.6251 (pp) outliers start: 47 outliers final: 32 residues processed: 331 average time/residue: 0.1305 time to fit residues: 69.4245 Evaluate side-chains 307 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123281 restraints weight = 27240.234| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.79 r_work: 0.3217 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20544 Z= 0.211 Angle : 0.617 11.319 27876 Z= 0.298 Chirality : 0.040 0.183 3148 Planarity : 0.004 0.044 3420 Dihedral : 6.872 65.375 2772 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.33 % Allowed : 19.55 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2428 helix: 1.73 (0.14), residues: 1468 sheet: -1.75 (0.49), residues: 92 loop : -1.44 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 687 TYR 0.015 0.002 TYR A 455 PHE 0.021 0.002 PHE A 405 TRP 0.036 0.001 TRP D 715 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00512 (20544) covalent geometry : angle 0.61725 (27876) hydrogen bonds : bond 0.03599 ( 1072) hydrogen bonds : angle 3.83062 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.5524 (p90) REVERT: A 92 LEU cc_start: 0.7501 (mm) cc_final: 0.6581 (pp) REVERT: A 473 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 537 LEU cc_start: 0.7973 (mt) cc_final: 0.7352 (mt) REVERT: A 647 GLU cc_start: 0.9057 (tt0) cc_final: 0.8441 (mt-10) REVERT: A 670 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7700 (tp30) REVERT: B 39 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6039 (p90) REVERT: B 92 LEU cc_start: 0.7676 (mt) cc_final: 0.7373 (mt) REVERT: B 305 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7984 (tt0) REVERT: B 383 GLN cc_start: 0.8337 (tp40) cc_final: 0.8070 (tt0) REVERT: B 645 MET cc_start: 0.8689 (tmm) cc_final: 0.7799 (tmm) REVERT: C 39 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.5829 (p90) REVERT: C 92 LEU cc_start: 0.7673 (mt) cc_final: 0.7370 (mt) REVERT: C 455 TYR cc_start: 0.9244 (t80) cc_final: 0.8948 (t80) REVERT: C 634 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: C 645 MET cc_start: 0.8516 (tmm) cc_final: 0.8045 (tmm) REVERT: C 670 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: D 39 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.5468 (p90) REVERT: D 92 LEU cc_start: 0.7707 (mt) cc_final: 0.6365 (pp) REVERT: D 670 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7770 (tp30) outliers start: 50 outliers final: 34 residues processed: 305 average time/residue: 0.1302 time to fit residues: 64.8192 Evaluate side-chains 297 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 224 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126526 restraints weight = 27202.967| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.87 r_work: 0.3264 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20544 Z= 0.120 Angle : 0.555 9.518 27876 Z= 0.269 Chirality : 0.037 0.169 3148 Planarity : 0.003 0.046 3420 Dihedral : 6.272 59.243 2772 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.82 % Allowed : 20.48 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2428 helix: 2.01 (0.14), residues: 1444 sheet: -1.73 (0.49), residues: 92 loop : -1.20 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.015 0.001 TYR A 455 PHE 0.022 0.001 PHE A 405 TRP 0.039 0.001 TRP D 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00288 (20544) covalent geometry : angle 0.55478 (27876) hydrogen bonds : bond 0.03157 ( 1072) hydrogen bonds : angle 3.66188 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.5475 (p90) REVERT: A 92 LEU cc_start: 0.7348 (mm) cc_final: 0.6470 (pp) REVERT: A 473 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 528 MET cc_start: 0.8449 (ptm) cc_final: 0.8216 (ttp) REVERT: A 647 GLU cc_start: 0.8948 (tt0) cc_final: 0.8356 (mt-10) REVERT: B 39 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5983 (p90) REVERT: B 92 LEU cc_start: 0.7657 (mt) cc_final: 0.6365 (pp) REVERT: B 305 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7901 (tt0) REVERT: B 383 GLN cc_start: 0.8294 (tp40) cc_final: 0.8022 (tt0) REVERT: B 634 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: B 645 MET cc_start: 0.8620 (tmm) cc_final: 0.8175 (ttm) REVERT: C 39 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.5715 (p90) REVERT: C 92 LEU cc_start: 0.7636 (mt) cc_final: 0.6305 (pp) REVERT: C 235 GLN cc_start: 0.7874 (mt0) cc_final: 0.7622 (mt0) REVERT: C 455 TYR cc_start: 0.9176 (t80) cc_final: 0.8861 (t80) REVERT: C 545 LEU cc_start: 0.9465 (mm) cc_final: 0.9209 (mt) REVERT: C 634 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: C 645 MET cc_start: 0.8532 (tmm) cc_final: 0.8161 (tmm) REVERT: C 670 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: D 39 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.5352 (p90) REVERT: D 92 LEU cc_start: 0.7644 (mt) cc_final: 0.6253 (pp) REVERT: D 519 PHE cc_start: 0.8238 (m-10) cc_final: 0.8024 (m-10) REVERT: D 670 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7659 (tp30) outliers start: 39 outliers final: 31 residues processed: 304 average time/residue: 0.1383 time to fit residues: 67.5860 Evaluate side-chains 305 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 95 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123023 restraints weight = 27315.141| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.85 r_work: 0.3211 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20544 Z= 0.176 Angle : 0.597 10.591 27876 Z= 0.289 Chirality : 0.039 0.173 3148 Planarity : 0.004 0.048 3420 Dihedral : 6.698 62.176 2772 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.14 % Allowed : 20.34 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2428 helix: 1.89 (0.14), residues: 1444 sheet: -1.78 (0.49), residues: 92 loop : -1.22 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.011 0.001 TYR B 544 PHE 0.022 0.001 PHE A 405 TRP 0.039 0.001 TRP A 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00428 (20544) covalent geometry : angle 0.59740 (27876) hydrogen bonds : bond 0.03472 ( 1072) hydrogen bonds : angle 3.77843 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4762.13 seconds wall clock time: 82 minutes 18.02 seconds (4938.02 seconds total)