Starting phenix.real_space_refine on Thu Jul 2 10:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2026/7xt6_33440.cif" } resolution = 3.63 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= 0.068 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 40 5.16 5 C 5067 2.51 5 N 1342 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1072 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 125} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2781 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 336} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1120 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2785 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 338} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.56, per 1000 atoms: 0.19 Number of scatterers: 8040 At special positions: 0 Unit cell: (71.5, 105.6, 191.4, 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 40 16.00 O 1591 8.00 N 1342 7.00 C 5067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 380 " - pdb=" SG CYS B 439 " distance=2.04 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 549 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 122 " distance=2.04 Simple disulfide: pdb=" SG CYS D 270 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 380 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 549 " distance=2.04 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN F 4 " - " NAG F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 201 " - " ASN A 73 " " NAG A 202 " - " ASN A 57 " " NAG A 203 " - " ASN A 63 " " NAG A 204 " - " ASN A 97 " " NAG A 205 " - " ASN A 88 " " NAG A 206 " - " ASN A 112 " " NAG B 701 " - " ASN B 345 " " NAG B 702 " - " ASN B 408 " " NAG C 201 " - " ASN C 101 " " NAG C 202 " - " ASN C 73 " " NAG D 701 " - " ASN D 345 " " NAG D 702 " - " ASN D 408 " " NAG F 1 " - " ASN B 415 " " NAG G 1 " - " ASN D 415 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 271.2 milliseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 24 sheets defined 19.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.795A pdb=" N ASN A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.526A pdb=" N ARG A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.515A pdb=" N TRP B 431 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.542A pdb=" N ASN B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 581 through 607 removed outlier: 3.631A pdb=" N ALA B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 594 " --> pdb=" O PHE B 590 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 181 removed outlier: 3.535A pdb=" N LEU C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Proline residue: C 176 - end of helix Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.569A pdb=" N ILE D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.700A pdb=" N ASN D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.766A pdb=" N LEU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 480 " --> pdb=" O GLN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.681A pdb=" N ASN D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 576 through 608 removed outlier: 3.662A pdb=" N VAL D 592 " --> pdb=" O SER D 588 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 596 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.807A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.812A pdb=" N ILE A 93 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 83 removed outlier: 6.387A pdb=" N PHE A 80 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 68 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 82 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 103 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.503A pdb=" N LYS B 248 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 273 " --> pdb=" O LYS B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.852A pdb=" N SER B 316 " --> pdb=" O CYS B 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.531A pdb=" N THR B 379 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE B 418 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 394 through 396 Processing sheet with id=AB1, first strand: chain 'B' and resid 466 through 470 removed outlier: 3.618A pdb=" N THR B 490 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 487 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 532 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 498 through 500 removed outlier: 3.631A pdb=" N THR B 561 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 502 through 503 removed outlier: 3.503A pdb=" N GLN B 503 " --> pdb=" O GLN B 506 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.648A pdb=" N MET B 519 " --> pdb=" O PHE B 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.693A pdb=" N ILE C 53 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N MET C 143 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG C 55 " --> pdb=" O MET C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.722A pdb=" N TYR C 133 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 248 through 252 removed outlier: 3.810A pdb=" N THR D 273 " --> pdb=" O LYS D 248 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 320 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 280 through 286 removed outlier: 3.503A pdb=" N CYS D 333 " --> pdb=" O GLN D 344 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'D' and resid 360 through 363 removed outlier: 3.748A pdb=" N PHE D 361 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 379 " --> pdb=" O ILE D 363 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR D 379 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA D 424 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU D 381 " --> pdb=" O GLY D 422 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY D 422 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N THR D 383 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA D 420 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D 385 " --> pdb=" O PHE D 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 392 through 396 Processing sheet with id=AC4, first strand: chain 'D' and resid 466 through 470 removed outlier: 3.737A pdb=" N ASP D 466 " --> pdb=" O THR D 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 490 " --> pdb=" O ASP D 466 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR D 528 " --> pdb=" O GLY D 491 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 466 through 470 removed outlier: 3.737A pdb=" N ASP D 466 " --> pdb=" O THR D 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 490 " --> pdb=" O ASP D 466 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR D 528 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 519 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 506 through 507 removed outlier: 3.672A pdb=" N GLN D 503 " --> pdb=" O GLN D 506 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR D 561 " --> pdb=" O VAL D 551 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 672 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: 0.78 Time building geometry restraints manager: 0.60 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: 2578 1.34 - 1.46: 1934 1.46 - 1.58: 3656 1.58 - 1.71: 1 1.71 - 1.83: 56 Bond restraints: 8225 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.592 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.459 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 8220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 11017 2.68 - 5.35: 166 5.35 - 8.03: 24 8.03 - 10.70: 2 10.70 - 13.38: 2 Bond angle restraints: 11211 Sorted by residual: angle pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" CD PRO A 129 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.91e+01 angle pdb=" N PRO A 128 " pdb=" CA PRO A 128 " pdb=" C PRO A 128 " ideal model delta sigma weight residual 110.70 115.41 -4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N GLY C 137 " pdb=" CA GLY C 137 " pdb=" C GLY C 137 " ideal model delta sigma weight residual 112.22 118.85 -6.63 1.74e+00 3.30e-01 1.45e+01 angle pdb=" C VAL B 565 " pdb=" N ASP B 566 " pdb=" CA ASP B 566 " ideal model delta sigma weight residual 121.90 117.15 4.75 1.26e+00 6.30e-01 1.42e+01 angle pdb=" CB PRO A 132 " pdb=" CG PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 106.10 94.17 11.93 3.20e+00 9.77e-02 1.39e+01 ... (remaining 11206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4106 17.12 - 34.24: 522 34.24 - 51.35: 120 51.35 - 68.47: 31 68.47 - 85.59: 11 Dihedral angle restraints: 4790 sinusoidal: 1885 harmonic: 2905 Sorted by residual: dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 333 " pdb=" CB CYS B 333 " ideal model delta sinusoidal sigma weight residual 93.00 178.25 -85.25 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 175.03 -82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CA ARG A 131 " pdb=" C ARG A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual 180.00 -144.79 -35.21 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 4787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1336 0.144 - 0.289: 9 0.289 - 0.433: 0 0.433 - 0.577: 0 0.577 - 0.721: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 415 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG A 205 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 205 " pdb=" O5 NAG A 205 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1343 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 253 " 0.051 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 254 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 254 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 254 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 131 " 0.043 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO A 132 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 470 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 471 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 471 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 471 " -0.034 5.00e-02 4.00e+02 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 492 2.73 - 3.27: 7594 3.27 - 3.81: 12030 3.81 - 4.36: 13091 4.36 - 4.90: 23584 Nonbonded interactions: 56791 Sorted by model distance: nonbonded pdb=" N GLN D 506 " pdb=" OE1 GLN D 506 " model vdw 2.182 3.120 nonbonded pdb=" NH2 ARG C 95 " pdb=" OD2 ASP C 116 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR D 356 " pdb=" OD2 ASP D 445 " model vdw 2.229 3.040 nonbonded pdb=" N GLU A 138 " pdb=" OE1 GLU A 138 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR D 373 " pdb=" OG SER D 375 " model vdw 2.275 3.040 ... (remaining 56786 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 'B' and (resid 245 through 302 or (resid 303 through 304 and (name N or n \ ame CA or name C or name O or name CB )) or resid 305 through 352 or (resid 353 \ through 355 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 6 through 357 or (resid 358 through 359 and (name N or name CA or name C or name \ O or name CB )) or resid 360 or (resid 361 through 362 and (name N or name CA o \ r name C or name O or name CB )) or resid 363 through 395 or (resid 396 and (nam \ e N or name CA or name C or name O or name CB )) or resid 397 through 403 or (re \ sid 404 and (name N or name CA or name C or name O or name CB )) or resid 405 th \ rough 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) \ or resid 414 through 435 or (resid 436 and (name N or name CA or name C or name \ O or name CB )) or resid 437 through 443 or (resid 444 and (name N or name CA o \ r name C or name O or name CB )) or resid 445 through 702)) selection = (chain 'D' and (resid 245 through 247 or (resid 248 and (name N or name CA or na \ me C or name O or name CB )) or resid 249 through 255 or (resid 256 and (name N \ or name CA or name C or name O or name CB )) or resid 257 through 283 or (resid \ 284 and (name N or name CA or name C or name O or name CB )) or resid 285 throug \ h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 331 or (resid 332 and (name N or name CA or name C or name O o \ r name CB )) or resid 333 through 347 or (resid 348 through 349 and (name N or n \ ame CA or name C or name O or name CB )) or resid 350 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 41 \ 6 or (resid 417 and (name N or name CA or name C or name O or name CB )) or resi \ d 418 through 607 or resid 701 through 702)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.005 0.066 8256 Z= 0.219 Angle : 0.861 13.377 11294 Z= 0.418 Chirality : 0.052 0.721 1346 Planarity : 0.005 0.079 1418 Dihedral : 16.202 85.588 2874 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.81 % Allowed : 24.25 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % 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: -2.04 (0.27), residues: 995 helix: 0.97 (0.43), residues: 156 sheet: -1.19 (0.29), residues: 332 loop : -2.26 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.013 0.001 TYR D 600 PHE 0.017 0.002 PHE B 418 TRP 0.039 0.002 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 ( 8225) covalent geometry : angle 0.81446 / 0.41 (11211) SS BOND : bond 0.00571 / 0.31 ( 10) SS BOND : angle 1.40585 / 0.78 ( 20) hydrogen bonds : bond 0.23838 / 16.42 ( 240) hydrogen bonds : angle 8.28287 / 5.92 ( 672) link_ALPHA1-3 : bond 0.00254 / 0.12 ( 2) link_ALPHA1-3 : angle 1.91137 / 0.76 ( 6) link_BETA1-2 : bond 0.00374 / 0.20 ( 1) link_BETA1-2 : angle 0.69825 / 0.31 ( 3) link_BETA1-4 : bond 0.00743 / 0.37 ( 4) link_BETA1-4 : angle 3.39125 / 1.46 ( 12) link_NAG-ASN : bond 0.00614 / 0.29 ( 14) link_NAG-ASN : angle 4.17210 / 2.00 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.232 Fit side-chains REVERT: B 454 ILE cc_start: 0.8027 (tp) cc_final: 0.7801 (pt) REVERT: B 578 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: D 506 GLN cc_start: 0.7981 (pm20) cc_final: 0.6797 (mm-40) outliers start: 7 outliers final: 2 residues processed: 81 average time/residue: 0.0771 time to fit residues: 8.5173 Evaluate side-chains 74 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain D residue 431 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 281 GLN ** B 337 HIS ** 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 = 0.4245 r_free = 0.4245 target = 0.195602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123556 restraints weight = 11087.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125507 restraints weight = 8931.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125707 restraints weight = 7473.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125804 restraints weight = 7427.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125871 restraints weight = 7327.923| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8256 Z= 0.232 Angle : 0.819 13.282 11294 Z= 0.408 Chirality : 0.050 0.335 1346 Planarity : 0.006 0.065 1418 Dihedral : 6.096 41.475 1072 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 5.22 % Allowed : 22.74 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -2.15 (0.27), residues: 995 helix: 0.72 (0.42), residues: 172 sheet: -1.11 (0.29), residues: 326 loop : -2.49 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 474 TYR 0.024 0.002 TYR D 547 PHE 0.018 0.002 PHE B 492 TRP 0.016 0.002 TRP C 47 HIS 0.008 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 ( 8225) covalent geometry : angle 0.78000 / 0.40 (11211) SS BOND : bond 0.01040 / 0.56 ( 10) SS BOND : angle 2.14298 / 1.19 ( 20) hydrogen bonds : bond 0.06096 / 4.19 ( 240) hydrogen bonds : angle 6.49229 / 4.61 ( 672) link_ALPHA1-3 : bond 0.00774 / 0.40 ( 2) link_ALPHA1-3 : angle 2.26474 / 1.09 ( 6) link_BETA1-2 : bond 0.00900 / 0.47 ( 1) link_BETA1-2 : angle 2.00343 / 0.92 ( 3) link_BETA1-4 : bond 0.00703 / 0.35 ( 4) link_BETA1-4 : angle 2.79901 / 1.25 ( 12) link_NAG-ASN : bond 0.00588 / 0.32 ( 14) link_NAG-ASN : angle 3.56177 / 1.82 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 71 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 470 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 535 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8632 (t) REVERT: B 578 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 469 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8718 (tt) REVERT: D 547 TYR cc_start: 0.8683 (m-80) cc_final: 0.8475 (m-80) outliers start: 45 outliers final: 26 residues processed: 108 average time/residue: 0.0642 time to fit residues: 10.0628 Evaluate side-chains 95 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 83 optimal weight: 0.0670 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4284 r_free = 0.4284 target = 0.200611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134128 restraints weight = 10948.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128224 restraints weight = 8541.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129954 restraints weight = 8660.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130221 restraints weight = 7175.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130400 restraints weight = 6782.434| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8256 Z= 0.136 Angle : 0.707 10.342 11294 Z= 0.348 Chirality : 0.046 0.277 1346 Planarity : 0.005 0.064 1418 Dihedral : 5.836 48.007 1070 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.64 % Allowed : 24.25 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -2.00 (0.27), residues: 995 helix: 0.84 (0.41), residues: 169 sheet: -0.90 (0.30), residues: 322 loop : -2.46 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 474 TYR 0.020 0.001 TYR D 547 PHE 0.011 0.001 PHE B 498 TRP 0.017 0.001 TRP C 47 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8225) covalent geometry : angle 0.67383 / 0.34 (11211) SS BOND : bond 0.00593 / 0.30 ( 10) SS BOND : angle 1.37500 / 0.77 ( 20) hydrogen bonds : bond 0.04939 / 3.38 ( 240) hydrogen bonds : angle 5.92510 / 4.22 ( 672) link_ALPHA1-3 : bond 0.00694 / 0.36 ( 2) link_ALPHA1-3 : angle 2.07630 / 0.92 ( 6) link_BETA1-2 : bond 0.00770 / 0.41 ( 1) link_BETA1-2 : angle 1.67151 / 0.66 ( 3) link_BETA1-4 : bond 0.00750 / 0.37 ( 4) link_BETA1-4 : angle 2.45172 / 1.09 ( 12) link_NAG-ASN : bond 0.00498 / 0.26 ( 14) link_NAG-ASN : angle 3.11166 / 1.60 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6812 (tp40) cc_final: 0.5455 (mt0) REVERT: C 67 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6661 (ppp) outliers start: 40 outliers final: 21 residues processed: 103 average time/residue: 0.0809 time to fit residues: 11.8194 Evaluate side-chains 88 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4301 r_free = 0.4301 target = 0.199143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151584 restraints weight = 10942.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129838 restraints weight = 16191.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131395 restraints weight = 13750.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132052 restraints weight = 9796.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132318 restraints weight = 9026.957| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8256 Z= 0.202 Angle : 0.757 9.544 11294 Z= 0.377 Chirality : 0.049 0.343 1346 Planarity : 0.005 0.069 1418 Dihedral : 5.970 48.497 1070 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 6.61 % Allowed : 22.97 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -2.05 (0.27), residues: 995 helix: 0.86 (0.42), residues: 169 sheet: -0.95 (0.29), residues: 326 loop : -2.51 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 474 TYR 0.027 0.002 TYR D 547 PHE 0.014 0.002 PHE B 492 TRP 0.018 0.001 TRP D 395 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 ( 8225) covalent geometry : angle 0.72547 / 0.37 (11211) SS BOND : bond 0.01089 / 0.66 ( 10) SS BOND : angle 2.00121 / 1.14 ( 20) hydrogen bonds : bond 0.05259 / 3.60 ( 240) hydrogen bonds : angle 5.82608 / 4.16 ( 672) link_ALPHA1-3 : bond 0.00582 / 0.30 ( 2) link_ALPHA1-3 : angle 2.22854 / 1.02 ( 6) link_BETA1-2 : bond 0.00775 / 0.41 ( 1) link_BETA1-2 : angle 2.13128 / 0.87 ( 3) link_BETA1-4 : bond 0.00767 / 0.38 ( 4) link_BETA1-4 : angle 2.59310 / 1.19 ( 12) link_NAG-ASN : bond 0.00494 / 0.26 ( 14) link_NAG-ASN : angle 2.98820 / 1.57 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 65 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6808 (tp40) cc_final: 0.5399 (mt0) REVERT: B 407 THR cc_start: 0.4279 (OUTLIER) cc_final: 0.4043 (p) REVERT: B 572 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: B 599 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: D 469 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8503 (tt) REVERT: D 506 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7541 (pm20) outliers start: 57 outliers final: 35 residues processed: 112 average time/residue: 0.0702 time to fit residues: 11.5848 Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 61 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4306 r_free = 0.4306 target = 0.199684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151540 restraints weight = 10875.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134914 restraints weight = 16513.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133692 restraints weight = 12392.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133889 restraints weight = 11382.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133796 restraints weight = 9870.979| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8256 Z= 0.181 Angle : 0.736 9.145 11294 Z= 0.365 Chirality : 0.048 0.279 1346 Planarity : 0.005 0.071 1418 Dihedral : 5.973 51.532 1070 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 6.26 % Allowed : 22.62 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -2.02 (0.27), residues: 995 helix: 0.93 (0.42), residues: 169 sheet: -0.91 (0.30), residues: 312 loop : -2.48 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.025 0.002 TYR D 547 PHE 0.014 0.002 PHE B 498 TRP 0.018 0.001 TRP D 395 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 8225) covalent geometry : angle 0.70578 / 0.36 (11211) SS BOND : bond 0.00882 / 0.51 ( 10) SS BOND : angle 1.86478 / 1.07 ( 20) hydrogen bonds : bond 0.04959 / 3.40 ( 240) hydrogen bonds : angle 5.68292 / 4.05 ( 672) link_ALPHA1-3 : bond 0.00577 / 0.30 ( 2) link_ALPHA1-3 : angle 2.22711 / 1.01 ( 6) link_BETA1-2 : bond 0.00775 / 0.41 ( 1) link_BETA1-2 : angle 2.05388 / 0.82 ( 3) link_BETA1-4 : bond 0.00732 / 0.37 ( 4) link_BETA1-4 : angle 2.41123 / 1.14 ( 12) link_NAG-ASN : bond 0.00507 / 0.26 ( 14) link_NAG-ASN : angle 2.86889 / 1.51 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 62 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6813 (tp40) cc_final: 0.5422 (mt0) REVERT: B 572 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: B 599 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: D 469 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8530 (tt) REVERT: D 506 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: D 600 TYR cc_start: 0.6897 (t80) cc_final: 0.6695 (t80) outliers start: 54 outliers final: 35 residues processed: 107 average time/residue: 0.0654 time to fit residues: 10.3953 Evaluate side-chains 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150999 restraints weight = 10812.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132212 restraints weight = 16233.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131868 restraints weight = 11937.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131301 restraints weight = 10457.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131613 restraints weight = 9686.026| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8256 Z= 0.208 Angle : 0.779 9.248 11294 Z= 0.385 Chirality : 0.051 0.448 1346 Planarity : 0.005 0.073 1418 Dihedral : 5.898 50.387 1068 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 6.61 % Allowed : 21.93 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -2.00 (0.27), residues: 995 helix: 0.97 (0.42), residues: 168 sheet: -0.99 (0.30), residues: 311 loop : -2.41 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.029 0.002 TYR D 547 PHE 0.016 0.002 PHE B 418 TRP 0.027 0.002 TRP D 395 HIS 0.008 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 8225) covalent geometry : angle 0.74848 / 0.38 (11211) SS BOND : bond 0.00936 / 0.51 ( 10) SS BOND : angle 2.02994 / 1.15 ( 20) hydrogen bonds : bond 0.05158 / 3.53 ( 240) hydrogen bonds : angle 5.67131 / 4.02 ( 672) link_ALPHA1-3 : bond 0.00485 / 0.25 ( 2) link_ALPHA1-3 : angle 2.27659 / 1.05 ( 6) link_BETA1-2 : bond 0.00831 / 0.44 ( 1) link_BETA1-2 : angle 2.16487 / 0.90 ( 3) link_BETA1-4 : bond 0.00646 / 0.32 ( 4) link_BETA1-4 : angle 2.49839 / 1.16 ( 12) link_NAG-ASN : bond 0.00452 / 0.24 ( 14) link_NAG-ASN : angle 2.98661 / 1.49 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 67 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6777 (tp40) cc_final: 0.5296 (mt0) REVERT: B 359 ARG cc_start: 0.7249 (mtm180) cc_final: 0.6991 (mtm180) REVERT: B 572 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: B 594 PHE cc_start: 0.7071 (t80) cc_final: 0.6726 (t80) REVERT: B 599 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: D 281 GLN cc_start: 0.7080 (pm20) cc_final: 0.6400 (pm20) REVERT: D 469 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8569 (tt) REVERT: D 506 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: D 600 TYR cc_start: 0.7026 (t80) cc_final: 0.6795 (t80) outliers start: 57 outliers final: 42 residues processed: 115 average time/residue: 0.0634 time to fit residues: 10.9472 Evaluate side-chains 111 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 506 GLN Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4318 r_free = 0.4318 target = 0.201164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154928 restraints weight = 10839.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138794 restraints weight = 15286.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133768 restraints weight = 11148.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134232 restraints weight = 10293.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134300 restraints weight = 9711.881| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8256 Z= 0.137 Angle : 0.701 8.575 11294 Z= 0.344 Chirality : 0.047 0.379 1346 Planarity : 0.005 0.071 1418 Dihedral : 5.713 54.373 1068 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.18 % Allowed : 24.59 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -1.88 (0.27), residues: 995 helix: 1.05 (0.42), residues: 169 sheet: -0.90 (0.30), residues: 313 loop : -2.34 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.028 0.001 TYR D 547 PHE 0.018 0.001 PHE D 342 TRP 0.029 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8225) covalent geometry : angle 0.67688 / 0.34 (11211) SS BOND : bond 0.00615 / 0.33 ( 10) SS BOND : angle 1.42656 / 0.80 ( 20) hydrogen bonds : bond 0.04370 / 2.98 ( 240) hydrogen bonds : angle 5.41097 / 3.84 ( 672) link_ALPHA1-3 : bond 0.00536 / 0.28 ( 2) link_ALPHA1-3 : angle 2.14287 / 0.95 ( 6) link_BETA1-2 : bond 0.00806 / 0.42 ( 1) link_BETA1-2 : angle 1.81149 / 0.71 ( 3) link_BETA1-4 : bond 0.00632 / 0.31 ( 4) link_BETA1-4 : angle 2.29831 / 1.10 ( 12) link_NAG-ASN : bond 0.00529 / 0.27 ( 14) link_NAG-ASN : angle 2.54972 / 1.30 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6692 (tp40) cc_final: 0.5383 (mt0) REVERT: B 572 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: B 593 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6999 (tp) REVERT: B 599 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: C 67 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6800 (ppp) REVERT: D 469 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 600 TYR cc_start: 0.7085 (t80) cc_final: 0.6854 (t80) outliers start: 36 outliers final: 26 residues processed: 97 average time/residue: 0.0572 time to fit residues: 8.2065 Evaluate side-chains 95 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 0.0370 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4254 r_free = 0.4254 target = 0.196441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138062 restraints weight = 10844.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135708 restraints weight = 13430.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129899 restraints weight = 9165.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129878 restraints weight = 8703.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130018 restraints weight = 8186.099| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8256 Z= 0.145 Angle : 0.708 8.919 11294 Z= 0.348 Chirality : 0.047 0.294 1346 Planarity : 0.005 0.070 1418 Dihedral : 5.561 51.093 1068 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.76 % Allowed : 23.90 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % 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: -1.81 (0.27), residues: 995 helix: 1.14 (0.42), residues: 169 sheet: -0.73 (0.30), residues: 304 loop : -2.39 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.028 0.001 TYR D 547 PHE 0.014 0.001 PHE B 418 TRP 0.018 0.001 TRP D 395 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8225) covalent geometry : angle 0.68466 / 0.34 (11211) SS BOND : bond 0.00698 / 0.39 ( 10) SS BOND : angle 1.52703 / 0.86 ( 20) hydrogen bonds : bond 0.04383 / 3.00 ( 240) hydrogen bonds : angle 5.31242 / 3.78 ( 672) link_ALPHA1-3 : bond 0.00533 / 0.28 ( 2) link_ALPHA1-3 : angle 2.10348 / 0.95 ( 6) link_BETA1-2 : bond 0.00856 / 0.45 ( 1) link_BETA1-2 : angle 1.84540 / 0.75 ( 3) link_BETA1-4 : bond 0.00638 / 0.32 ( 4) link_BETA1-4 : angle 2.25297 / 1.07 ( 12) link_NAG-ASN : bond 0.00370 / 0.20 ( 14) link_NAG-ASN : angle 2.47016 / 1.30 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6745 (tp40) cc_final: 0.5355 (mt0) REVERT: B 599 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: C 67 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6738 (ppp) REVERT: C 165 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7126 (mt0) outliers start: 41 outliers final: 32 residues processed: 96 average time/residue: 0.0676 time to fit residues: 9.6081 Evaluate side-chains 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 71 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 68 optimal weight: 0.0470 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4304 r_free = 0.4304 target = 0.201836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137264 restraints weight = 10936.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133311 restraints weight = 8169.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136058 restraints weight = 7406.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135729 restraints weight = 5856.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135737 restraints weight = 6073.681| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8256 Z= 0.114 Angle : 0.665 8.332 11294 Z= 0.325 Chirality : 0.045 0.258 1346 Planarity : 0.005 0.064 1418 Dihedral : 5.365 53.032 1068 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.25 % Allowed : 25.87 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % 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: -1.65 (0.27), residues: 995 helix: 1.08 (0.41), residues: 169 sheet: -0.58 (0.30), residues: 309 loop : -2.24 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.027 0.001 TYR D 547 PHE 0.013 0.001 PHE D 342 TRP 0.043 0.001 TRP D 395 HIS 0.003 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8225) covalent geometry : angle 0.64808 / 0.32 (11211) SS BOND : bond 0.00385 / 0.24 ( 10) SS BOND : angle 0.77680 / 0.43 ( 20) hydrogen bonds : bond 0.03626 / 2.48 ( 240) hydrogen bonds : angle 5.08552 / 3.64 ( 672) link_ALPHA1-3 : bond 0.00590 / 0.30 ( 2) link_ALPHA1-3 : angle 1.89704 / 0.83 ( 6) link_BETA1-2 : bond 0.00798 / 0.42 ( 1) link_BETA1-2 : angle 1.36741 / 0.54 ( 3) link_BETA1-4 : bond 0.00734 / 0.36 ( 4) link_BETA1-4 : angle 2.12689 / 1.07 ( 12) link_NAG-ASN : bond 0.00437 / 0.22 ( 14) link_NAG-ASN : angle 2.16566 / 1.14 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6846 (tp40) cc_final: 0.5426 (mt0) REVERT: B 486 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8444 (m) REVERT: B 593 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6895 (tp) REVERT: C 67 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6843 (ppp) REVERT: C 165 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: D 469 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (tt) outliers start: 28 outliers final: 20 residues processed: 92 average time/residue: 0.0759 time to fit residues: 9.8706 Evaluate side-chains 93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 0.0070 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.4297 r_free = 0.4297 target = 0.201389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142677 restraints weight = 11047.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141467 restraints weight = 12876.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140989 restraints weight = 10458.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138145 restraints weight = 9965.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139336 restraints weight = 8689.130| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8256 Z= 0.121 Angle : 0.675 8.450 11294 Z= 0.331 Chirality : 0.045 0.270 1346 Planarity : 0.005 0.058 1418 Dihedral : 5.184 49.136 1068 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.13 % Allowed : 25.99 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % 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: -1.57 (0.27), residues: 995 helix: 1.16 (0.41), residues: 169 sheet: -0.47 (0.30), residues: 316 loop : -2.28 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.041 0.001 TYR D 547 PHE 0.018 0.001 PHE D 252 TRP 0.053 0.001 TRP D 395 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8225) covalent geometry : angle 0.65689 / 0.33 (11211) SS BOND : bond 0.00480 / 0.27 ( 10) SS BOND : angle 1.17943 / 0.68 ( 20) hydrogen bonds : bond 0.03727 / 2.55 ( 240) hydrogen bonds : angle 5.01830 / 3.56 ( 672) link_ALPHA1-3 : bond 0.00532 / 0.27 ( 2) link_ALPHA1-3 : angle 1.99182 / 0.87 ( 6) link_BETA1-2 : bond 0.00762 / 0.40 ( 1) link_BETA1-2 : angle 1.47523 / 0.58 ( 3) link_BETA1-4 : bond 0.00693 / 0.34 ( 4) link_BETA1-4 : angle 2.04368 / 0.97 ( 12) link_NAG-ASN : bond 0.00414 / 0.22 ( 14) link_NAG-ASN : angle 2.22037 / 1.18 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6607 (tp40) cc_final: 0.5313 (mt0) REVERT: B 359 ARG cc_start: 0.6831 (ptp-170) cc_final: 0.6256 (mtm180) REVERT: B 486 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8320 (m) REVERT: B 593 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7130 (tp) REVERT: C 67 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6858 (ppp) REVERT: C 165 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7230 (mt0) outliers start: 27 outliers final: 20 residues processed: 88 average time/residue: 0.0603 time to fit residues: 7.8280 Evaluate side-chains 91 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.204128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157918 restraints weight = 10948.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140530 restraints weight = 16899.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137398 restraints weight = 11594.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137609 restraints weight = 10890.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138160 restraints weight = 9861.360| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8256 Z= 0.143 Angle : 0.697 8.573 11294 Z= 0.344 Chirality : 0.046 0.225 1346 Planarity : 0.005 0.068 1418 Dihedral : 5.357 52.308 1068 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.25 % Allowed : 25.99 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % 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: -1.55 (0.27), residues: 995 helix: 1.26 (0.42), residues: 169 sheet: -0.48 (0.30), residues: 316 loop : -2.28 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.011 0.001 TYR D 600 PHE 0.017 0.002 PHE D 252 TRP 0.066 0.002 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8225) covalent geometry : angle 0.67885 / 0.34 (11211) SS BOND : bond 0.00715 / 0.40 ( 10) SS BOND : angle 1.57221 / 0.90 ( 20) hydrogen bonds : bond 0.04080 / 2.80 ( 240) hydrogen bonds : angle 5.10690 / 3.62 ( 672) link_ALPHA1-3 : bond 0.00463 / 0.24 ( 2) link_ALPHA1-3 : angle 2.06137 / 0.91 ( 6) link_BETA1-2 : bond 0.00701 / 0.37 ( 1) link_BETA1-2 : angle 1.66724 / 0.65 ( 3) link_BETA1-4 : bond 0.00682 / 0.34 ( 4) link_BETA1-4 : angle 2.02840 / 0.97 ( 12) link_NAG-ASN : bond 0.00402 / 0.22 ( 14) link_NAG-ASN : angle 2.12557 / 1.18 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1436.99 seconds wall clock time: 25 minutes 25.53 seconds (1525.53 seconds total)