Starting phenix.real_space_refine on Tue Mar 3 19:15:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xt6_33440/03_2026/7xt6_33440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt6_33440/03_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_33440/03_2026/7xt6_33440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2026/7xt6_33440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2026/7xt6_33440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt6_33440/03_2026/7xt6_33440.map" } 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-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.95, per 1000 atoms: 0.24 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: 0.70 Conformation dependent library (CDL) restraints added in 300.6 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: 0.29 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: 1.22 Time building geometry restraints manager: 0.91 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 - 21.86: 4676 21.86 - 43.71: 441 43.71 - 65.57: 72 65.57 - 87.43: 20 87.43 - 109.28: 14 Dihedral angle restraints: 5223 sinusoidal: 2318 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 5220 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 17.764 109.282 3307 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 covalent geometry : bond 0.00470 ( 8225) covalent geometry : angle 0.81446 (11211) SS BOND : bond 0.00571 ( 10) SS BOND : angle 1.40585 ( 20) hydrogen bonds : bond 0.23838 ( 240) hydrogen bonds : angle 8.28287 ( 672) link_ALPHA1-3 : bond 0.00254 ( 2) link_ALPHA1-3 : angle 1.91137 ( 6) link_BETA1-2 : bond 0.00374 ( 1) link_BETA1-2 : angle 0.69825 ( 3) link_BETA1-4 : bond 0.00743 ( 4) link_BETA1-4 : angle 3.39125 ( 12) link_NAG-ASN : bond 0.00614 ( 14) link_NAG-ASN : angle 4.17210 ( 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 : 0.271 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: 0.0993 time to fit residues: 10.9255 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 : 0.255 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4246 r_free = 0.4246 target = 0.195630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121372 restraints weight = 11048.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124393 restraints weight = 8257.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126042 restraints weight = 6936.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127252 restraints weight = 6266.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127255 restraints weight = 5889.325| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0987 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 : 0.833 13.135 11294 Z= 0.412 Chirality : 0.051 0.376 1346 Planarity : 0.006 0.065 1418 Dihedral : 11.887 98.682 1505 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 5.22 % Allowed : 22.85 % Favored : 71.93 % 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: -2.14 (0.27), residues: 995 helix: 0.74 (0.42), residues: 172 sheet: -1.10 (0.29), residues: 326 loop : -2.49 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 474 TYR 0.023 0.002 TYR D 547 PHE 0.018 0.002 PHE B 492 TRP 0.018 0.002 TRP D 395 HIS 0.008 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8225) covalent geometry : angle 0.78898 (11211) SS BOND : bond 0.01040 ( 10) SS BOND : angle 2.12194 ( 20) hydrogen bonds : bond 0.05889 ( 240) hydrogen bonds : angle 6.49692 ( 672) link_ALPHA1-3 : bond 0.01102 ( 2) link_ALPHA1-3 : angle 2.74371 ( 6) link_BETA1-2 : bond 0.00835 ( 1) link_BETA1-2 : angle 1.94157 ( 3) link_BETA1-4 : bond 0.00397 ( 4) link_BETA1-4 : angle 3.37662 ( 12) link_NAG-ASN : bond 0.00560 ( 14) link_NAG-ASN : angle 3.72107 ( 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 115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 70 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 470 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 535 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8630 (t) REVERT: B 578 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: D 469 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8710 (tt) REVERT: D 547 TYR cc_start: 0.8678 (m-80) cc_final: 0.8464 (m-80) outliers start: 45 outliers final: 26 residues processed: 107 average time/residue: 0.0756 time to fit residues: 11.6625 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.0040 chunk 22 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4266 r_free = 0.4266 target = 0.197824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131381 restraints weight = 10899.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126490 restraints weight = 8396.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128757 restraints weight = 7844.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128864 restraints weight = 7017.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129085 restraints weight = 6802.918| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1249 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= 0.151 Angle : 0.739 10.181 11294 Z= 0.360 Chirality : 0.048 0.340 1346 Planarity : 0.005 0.063 1418 Dihedral : 10.383 92.915 1503 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.57 % Allowed : 23.20 % 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: -2.04 (0.27), residues: 995 helix: 0.81 (0.41), residues: 169 sheet: -0.93 (0.30), residues: 322 loop : -2.47 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 474 TYR 0.019 0.001 TYR D 547 PHE 0.013 0.001 PHE B 492 TRP 0.017 0.001 TRP C 47 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8225) covalent geometry : angle 0.69887 (11211) SS BOND : bond 0.00717 ( 10) SS BOND : angle 1.51155 ( 20) hydrogen bonds : bond 0.05103 ( 240) hydrogen bonds : angle 5.93520 ( 672) link_ALPHA1-3 : bond 0.00956 ( 2) link_ALPHA1-3 : angle 2.29421 ( 6) link_BETA1-2 : bond 0.00689 ( 1) link_BETA1-2 : angle 1.82056 ( 3) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 3.23626 ( 12) link_NAG-ASN : bond 0.00766 ( 14) link_NAG-ASN : angle 3.40239 ( 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 121 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 73 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6824 (tp40) cc_final: 0.5498 (mt0) REVERT: C 67 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6614 (ppp) REVERT: D 536 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7491 (m) outliers start: 48 outliers final: 26 residues processed: 111 average time/residue: 0.0780 time to fit residues: 12.3254 Evaluate side-chains 94 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 251 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 467 VAL 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 426 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 536 VAL 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: 0.9980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4243 r_free = 0.4243 target = 0.195289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137677 restraints weight = 10974.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135198 restraints weight = 13659.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126469 restraints weight = 8430.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127258 restraints weight = 9309.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127887 restraints weight = 8184.241| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8256 Z= 0.187 Angle : 0.762 9.092 11294 Z= 0.374 Chirality : 0.049 0.342 1346 Planarity : 0.005 0.068 1418 Dihedral : 9.480 88.030 1503 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 6.26 % Allowed : 22.85 % Favored : 70.88 % 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: -2.07 (0.27), residues: 995 helix: 0.87 (0.42), residues: 169 sheet: -0.99 (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 0.028 0.002 TYR D 547 PHE 0.020 0.002 PHE D 252 TRP 0.019 0.001 TRP D 395 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8225) covalent geometry : angle 0.72231 (11211) SS BOND : bond 0.00862 ( 10) SS BOND : angle 1.85930 ( 20) hydrogen bonds : bond 0.05058 ( 240) hydrogen bonds : angle 5.77094 ( 672) link_ALPHA1-3 : bond 0.00779 ( 2) link_ALPHA1-3 : angle 2.48148 ( 6) link_BETA1-2 : bond 0.00756 ( 1) link_BETA1-2 : angle 2.01122 ( 3) link_BETA1-4 : bond 0.00681 ( 4) link_BETA1-4 : angle 3.43598 ( 12) link_NAG-ASN : bond 0.00530 ( 14) link_NAG-ASN : angle 3.28499 ( 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 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 63 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6787 (tp40) cc_final: 0.5374 (mt0) REVERT: B 599 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: D 469 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8529 (tt) outliers start: 54 outliers final: 36 residues processed: 107 average time/residue: 0.0683 time to fit residues: 10.8843 Evaluate side-chains 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 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 415 ASN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4292 r_free = 0.4292 target = 0.198365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151000 restraints weight = 10862.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130022 restraints weight = 15999.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132178 restraints weight = 13000.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131898 restraints weight = 9858.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132130 restraints weight = 9573.516| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8256 Z= 0.209 Angle : 0.781 8.967 11294 Z= 0.385 Chirality : 0.050 0.335 1346 Planarity : 0.005 0.070 1418 Dihedral : 8.760 79.455 1503 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 6.73 % Allowed : 22.16 % 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: -2.06 (0.27), residues: 995 helix: 0.94 (0.42), residues: 169 sheet: -1.00 (0.30), residues: 312 loop : -2.49 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.026 0.002 TYR D 547 PHE 0.019 0.002 PHE B 418 TRP 0.022 0.002 TRP D 395 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8225) covalent geometry : angle 0.74135 (11211) SS BOND : bond 0.00968 ( 10) SS BOND : angle 2.03405 ( 20) hydrogen bonds : bond 0.05194 ( 240) hydrogen bonds : angle 5.72848 ( 672) link_ALPHA1-3 : bond 0.00879 ( 2) link_ALPHA1-3 : angle 2.60425 ( 6) link_BETA1-2 : bond 0.00706 ( 1) link_BETA1-2 : angle 2.00407 ( 3) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 3.52894 ( 12) link_NAG-ASN : bond 0.00482 ( 14) link_NAG-ASN : angle 3.26403 ( 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 123 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 65 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6772 (tp40) cc_final: 0.5412 (mt0) REVERT: B 359 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6892 (mtm180) REVERT: B 599 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: C 162 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7104 (mp) REVERT: D 469 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8559 (tt) REVERT: D 600 TYR cc_start: 0.6985 (t80) cc_final: 0.6767 (t80) outliers start: 58 outliers final: 38 residues processed: 113 average time/residue: 0.0703 time to fit residues: 11.7652 Evaluate side-chains 102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 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 C residue 162 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4300 r_free = 0.4300 target = 0.199375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151035 restraints weight = 10821.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129857 restraints weight = 16676.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132010 restraints weight = 12386.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132512 restraints weight = 10128.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132605 restraints weight = 8659.334| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8256 Z= 0.172 Angle : 0.766 9.678 11294 Z= 0.371 Chirality : 0.050 0.426 1346 Planarity : 0.005 0.071 1418 Dihedral : 8.339 74.566 1501 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 6.15 % Allowed : 22.62 % 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: -1.99 (0.27), residues: 995 helix: 0.96 (0.42), residues: 169 sheet: -0.97 (0.29), residues: 314 loop : -2.42 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.027 0.002 TYR D 547 PHE 0.014 0.002 PHE B 498 TRP 0.023 0.001 TRP D 395 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8225) covalent geometry : angle 0.72622 (11211) SS BOND : bond 0.00803 ( 10) SS BOND : angle 1.74661 ( 20) hydrogen bonds : bond 0.04836 ( 240) hydrogen bonds : angle 5.59959 ( 672) link_ALPHA1-3 : bond 0.00782 ( 2) link_ALPHA1-3 : angle 2.53391 ( 6) link_BETA1-2 : bond 0.00747 ( 1) link_BETA1-2 : angle 1.92595 ( 3) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 3.44916 ( 12) link_NAG-ASN : bond 0.00472 ( 14) link_NAG-ASN : angle 3.32111 ( 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 118 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 65 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6761 (tp40) cc_final: 0.5416 (mt0) REVERT: B 593 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6927 (tp) REVERT: B 594 PHE cc_start: 0.7077 (t80) cc_final: 0.6680 (t80) REVERT: B 599 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: C 67 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6806 (ppp) REVERT: C 162 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6980 (mp) REVERT: D 469 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8511 (tt) REVERT: D 600 TYR cc_start: 0.6998 (t80) cc_final: 0.6766 (t80) outliers start: 53 outliers final: 41 residues processed: 109 average time/residue: 0.0666 time to fit residues: 10.8109 Evaluate side-chains 110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 253 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 438 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 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 VAL 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 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 C residue 162 ILE 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 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: 0.9980 chunk 96 optimal weight: 0.8980 chunk 85 optimal weight: 0.0570 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.201364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154777 restraints weight = 10822.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140554 restraints weight = 15823.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134672 restraints weight = 10300.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135018 restraints weight = 10533.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135709 restraints weight = 8965.382| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2155 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= 0.136 Angle : 0.724 8.950 11294 Z= 0.348 Chirality : 0.048 0.381 1346 Planarity : 0.005 0.071 1418 Dihedral : 7.810 68.497 1501 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.99 % Allowed : 24.36 % Favored : 70.65 % 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: -1.87 (0.27), residues: 995 helix: 1.04 (0.42), residues: 169 sheet: -0.89 (0.30), residues: 313 loop : -2.33 (0.26), residues: 513 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 0.017 0.001 PHE D 342 TRP 0.030 0.001 TRP D 395 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8225) covalent geometry : angle 0.68851 (11211) SS BOND : bond 0.00671 ( 10) SS BOND : angle 1.40372 ( 20) hydrogen bonds : bond 0.04318 ( 240) hydrogen bonds : angle 5.39569 ( 672) link_ALPHA1-3 : bond 0.00714 ( 2) link_ALPHA1-3 : angle 2.24039 ( 6) link_BETA1-2 : bond 0.00811 ( 1) link_BETA1-2 : angle 1.81190 ( 3) link_BETA1-4 : bond 0.00502 ( 4) link_BETA1-4 : angle 3.40248 ( 12) link_NAG-ASN : bond 0.00535 ( 14) link_NAG-ASN : angle 3.06401 ( 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 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6706 (tp40) cc_final: 0.5396 (mt0) REVERT: B 359 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6746 (mtm180) REVERT: B 599 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: C 67 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6809 (ppp) REVERT: C 162 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7037 (mp) REVERT: D 600 TYR cc_start: 0.7063 (t80) cc_final: 0.6846 (t80) outliers start: 43 outliers final: 35 residues processed: 101 average time/residue: 0.0720 time to fit residues: 10.7457 Evaluate side-chains 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 253 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 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 469 LEU 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 569 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE 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 67 MET 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 C residue 162 ILE 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 356 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 460 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 606 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: 5.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 59 optimal weight: 0.0370 chunk 90 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.0470 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4325 r_free = 0.4325 target = 0.202072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154341 restraints weight = 10818.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143260 restraints weight = 16747.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138149 restraints weight = 10113.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136960 restraints weight = 11154.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138010 restraints weight = 9725.379| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2327 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= 0.132 Angle : 0.709 8.634 11294 Z= 0.343 Chirality : 0.048 0.448 1346 Planarity : 0.005 0.068 1418 Dihedral : 7.372 63.612 1501 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 5.34 % Allowed : 23.43 % 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: -1.76 (0.27), residues: 995 helix: 1.11 (0.42), residues: 169 sheet: -0.69 (0.30), residues: 304 loop : -2.32 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.029 0.001 TYR D 547 PHE 0.014 0.001 PHE D 342 TRP 0.017 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8225) covalent geometry : angle 0.67631 (11211) SS BOND : bond 0.00611 ( 10) SS BOND : angle 1.36213 ( 20) hydrogen bonds : bond 0.04177 ( 240) hydrogen bonds : angle 5.27183 ( 672) link_ALPHA1-3 : bond 0.00759 ( 2) link_ALPHA1-3 : angle 2.29327 ( 6) link_BETA1-2 : bond 0.00700 ( 1) link_BETA1-2 : angle 1.75454 ( 3) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 3.35927 ( 12) link_NAG-ASN : bond 0.00467 ( 14) link_NAG-ASN : angle 2.79791 ( 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 114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 68 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6703 (tp40) cc_final: 0.5377 (mt0) REVERT: B 599 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: C 67 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6805 (ppp) REVERT: C 165 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7090 (mt0) outliers start: 46 outliers final: 37 residues processed: 103 average time/residue: 0.0700 time to fit residues: 10.6090 Evaluate side-chains 107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 146 THR 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 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 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 569 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE 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 67 MET Chi-restraints excluded: chain C residue 74 VAL 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 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 356 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 460 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4327 r_free = 0.4327 target = 0.202224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155453 restraints weight = 10886.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140835 restraints weight = 15652.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134762 restraints weight = 10005.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135596 restraints weight = 10137.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136572 restraints weight = 8862.116| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2416 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 : 0.722 8.756 11294 Z= 0.349 Chirality : 0.048 0.436 1346 Planarity : 0.005 0.070 1418 Dihedral : 7.136 57.706 1501 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 5.80 % Allowed : 23.43 % 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: -1.71 (0.27), residues: 995 helix: 1.13 (0.42), residues: 169 sheet: -0.72 (0.30), residues: 313 loop : -2.27 (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 0.013 0.001 PHE B 418 TRP 0.038 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8225) covalent geometry : angle 0.68994 (11211) SS BOND : bond 0.00615 ( 10) SS BOND : angle 1.42167 ( 20) hydrogen bonds : bond 0.04243 ( 240) hydrogen bonds : angle 5.27551 ( 672) link_ALPHA1-3 : bond 0.00776 ( 2) link_ALPHA1-3 : angle 2.24305 ( 6) link_BETA1-2 : bond 0.00763 ( 1) link_BETA1-2 : angle 1.79586 ( 3) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 3.35601 ( 12) link_NAG-ASN : bond 0.00451 ( 14) link_NAG-ASN : angle 2.81551 ( 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 118 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6695 (tp40) cc_final: 0.5359 (mt0) REVERT: A 126 ARG cc_start: 0.6402 (pmt-80) cc_final: 0.6138 (pmt-80) REVERT: B 599 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: C 67 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6830 (ppp) REVERT: C 165 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7257 (mt0) outliers start: 50 outliers final: 41 residues processed: 108 average time/residue: 0.0762 time to fit residues: 11.7116 Evaluate side-chains 109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 253 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 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 569 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE 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 67 MET Chi-restraints excluded: chain C residue 74 VAL 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 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 356 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 460 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4312 r_free = 0.4312 target = 0.200627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154057 restraints weight = 10830.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142338 restraints weight = 17393.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136888 restraints weight = 11149.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135894 restraints weight = 13311.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137846 restraints weight = 10871.104| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2568 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= 0.162 Angle : 0.744 8.960 11294 Z= 0.364 Chirality : 0.049 0.407 1346 Planarity : 0.005 0.066 1418 Dihedral : 6.874 50.800 1501 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 5.45 % Allowed : 23.55 % Favored : 71.00 % 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: -1.66 (0.27), residues: 995 helix: 1.19 (0.43), residues: 168 sheet: -0.70 (0.30), residues: 310 loop : -2.22 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.037 0.002 TYR D 547 PHE 0.014 0.001 PHE B 498 TRP 0.038 0.002 TRP D 395 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8225) covalent geometry : angle 0.71317 (11211) SS BOND : bond 0.00798 ( 10) SS BOND : angle 1.80183 ( 20) hydrogen bonds : bond 0.04518 ( 240) hydrogen bonds : angle 5.32698 ( 672) link_ALPHA1-3 : bond 0.00740 ( 2) link_ALPHA1-3 : angle 2.48837 ( 6) link_BETA1-2 : bond 0.00660 ( 1) link_BETA1-2 : angle 1.98428 ( 3) link_BETA1-4 : bond 0.00248 ( 4) link_BETA1-4 : angle 3.32573 ( 12) link_NAG-ASN : bond 0.00424 ( 14) link_NAG-ASN : angle 2.65210 ( 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 109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 62 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6719 (tp40) cc_final: 0.5288 (mt0) REVERT: B 599 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7256 (m-10) REVERT: C 165 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7243 (mt0) outliers start: 47 outliers final: 41 residues processed: 101 average time/residue: 0.0647 time to fit residues: 9.8127 Evaluate side-chains 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 253 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 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 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 569 THR 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 74 VAL 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 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 356 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 460 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4325 r_free = 0.4325 target = 0.201968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154272 restraints weight = 10746.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143065 restraints weight = 16253.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135091 restraints weight = 10995.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134996 restraints weight = 12359.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136643 restraints weight = 10128.073| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2680 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= 0.138 Angle : 0.717 8.688 11294 Z= 0.348 Chirality : 0.048 0.388 1346 Planarity : 0.005 0.085 1418 Dihedral : 6.614 55.138 1501 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.64 % Allowed : 24.36 % Favored : 71.00 % 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: -1.63 (0.27), residues: 995 helix: 1.16 (0.42), residues: 169 sheet: -0.63 (0.30), residues: 310 loop : -2.22 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.011 0.001 TYR D 600 PHE 0.017 0.001 PHE D 342 TRP 0.050 0.002 TRP D 395 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8225) covalent geometry : angle 0.68998 (11211) SS BOND : bond 0.00638 ( 10) SS BOND : angle 1.42350 ( 20) hydrogen bonds : bond 0.04157 ( 240) hydrogen bonds : angle 5.23997 ( 672) link_ALPHA1-3 : bond 0.00713 ( 2) link_ALPHA1-3 : angle 2.28055 ( 6) link_BETA1-2 : bond 0.00629 ( 1) link_BETA1-2 : angle 1.84581 ( 3) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 3.16633 ( 12) link_NAG-ASN : bond 0.00414 ( 14) link_NAG-ASN : angle 2.49084 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.58 seconds wall clock time: 28 minutes 26.24 seconds (1706.24 seconds total)