Starting phenix.real_space_refine on Wed Feb 12 19:31:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_33440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_33440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_33440.map" model { file = "/net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_33440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt6_33440/02_2025/7xt6_33440.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 5.57, per 1000 atoms: 0.69 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.93 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: 2.82 Time building geometry restraints manager: 2.55 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 607 or resid 701 through 7 \ 02)) 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- 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 8225 Z= 0.310 Angle : 0.814 13.377 11211 Z= 0.408 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 : 8.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (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 TRP 0.039 0.002 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.017 0.002 PHE B 418 TYR 0.013 0.001 TYR D 600 ARG 0.003 0.000 ARG B 359 *********************** 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 : 0.858 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: 0.2355 time to fit residues: 25.8376 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 : 0.832 ------------------------------------------------------------------------------- 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 82 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.199464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125844 restraints weight = 10874.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129434 restraints weight = 8654.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130357 restraints weight = 6703.615| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8225 Z= 0.227 Angle : 0.716 12.444 11211 Z= 0.360 Chirality : 0.049 0.374 1346 Planarity : 0.005 0.063 1418 Dihedral : 11.732 98.820 1505 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.60 % Allowed : 24.13 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 995 helix: 0.77 (0.42), residues: 172 sheet: -0.88 (0.30), residues: 325 loop : -2.44 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 395 HIS 0.005 0.001 HIS A 71 PHE 0.013 0.002 PHE B 418 TYR 0.024 0.001 TYR D 547 ARG 0.003 0.000 ARG C 55 *********************** 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 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 454 ILE cc_start: 0.8199 (tp) cc_final: 0.7989 (pt) REVERT: B 578 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: C 67 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6749 (ppp) REVERT: D 469 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8567 (tt) REVERT: D 506 GLN cc_start: 0.7714 (pm20) cc_final: 0.6937 (mm-40) outliers start: 31 outliers final: 15 residues processed: 93 average time/residue: 0.1891 time to fit residues: 24.7019 Evaluate side-chains 81 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 67 MET 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 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 40 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** B 443 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.194121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135758 restraints weight = 11037.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135827 restraints weight = 13614.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130198 restraints weight = 9530.715| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8225 Z= 0.429 Angle : 0.796 11.376 11211 Z= 0.405 Chirality : 0.052 0.341 1346 Planarity : 0.006 0.067 1418 Dihedral : 10.349 92.444 1503 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 6.38 % Allowed : 22.85 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.27), residues: 995 helix: 0.75 (0.42), residues: 172 sheet: -1.09 (0.29), residues: 329 loop : -2.58 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 395 HIS 0.009 0.002 HIS A 71 PHE 0.016 0.002 PHE B 418 TYR 0.026 0.002 TYR D 547 ARG 0.005 0.001 ARG B 474 *********************** 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 128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 73 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6769 (tp40) cc_final: 0.5259 (mt0) REVERT: B 359 ARG cc_start: 0.7194 (mtm180) cc_final: 0.6595 (mtm180) REVERT: B 470 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8503 (mt) REVERT: D 469 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8695 (tt) outliers start: 55 outliers final: 32 residues processed: 119 average time/residue: 0.1856 time to fit residues: 31.1795 Evaluate side-chains 100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 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 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 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.196059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138989 restraints weight = 10875.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135802 restraints weight = 13837.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127143 restraints weight = 8830.137| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8225 Z= 0.262 Angle : 0.705 9.216 11211 Z= 0.356 Chirality : 0.049 0.367 1346 Planarity : 0.005 0.068 1418 Dihedral : 9.474 87.602 1503 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 6.03 % Allowed : 23.43 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.27), residues: 995 helix: 0.81 (0.42), residues: 169 sheet: -1.00 (0.29), residues: 330 loop : -2.52 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 395 HIS 0.006 0.001 HIS A 71 PHE 0.013 0.001 PHE B 498 TYR 0.026 0.002 TYR D 547 ARG 0.004 0.000 ARG B 474 *********************** 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 120 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 68 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6775 (tp40) cc_final: 0.5365 (mt0) REVERT: B 407 THR cc_start: 0.4236 (OUTLIER) cc_final: 0.3941 (p) REVERT: B 599 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: C 67 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6717 (ppp) outliers start: 52 outliers final: 36 residues processed: 109 average time/residue: 0.1680 time to fit residues: 26.7368 Evaluate side-chains 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 599 PHE 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 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 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 502 MET 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 56 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.197600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140681 restraints weight = 10744.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136854 restraints weight = 13350.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131187 restraints weight = 9294.496| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8225 Z= 0.204 Angle : 0.681 8.609 11211 Z= 0.340 Chirality : 0.048 0.352 1346 Planarity : 0.005 0.068 1418 Dihedral : 8.846 81.621 1503 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 5.45 % Allowed : 23.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.27), residues: 995 helix: 0.94 (0.42), residues: 169 sheet: -0.89 (0.29), residues: 330 loop : -2.47 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.012 0.001 PHE B 498 TYR 0.025 0.001 TYR D 547 ARG 0.003 0.000 ARG B 474 *********************** 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 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6724 (tp40) cc_final: 0.5323 (mt0) REVERT: B 572 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: C 67 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6708 (ppp) REVERT: D 469 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8399 (tt) outliers start: 47 outliers final: 28 residues processed: 102 average time/residue: 0.1713 time to fit residues: 25.4728 Evaluate side-chains 93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain 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 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 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 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 82 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.200359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154245 restraints weight = 10681.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138873 restraints weight = 15391.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134307 restraints weight = 10881.939| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8225 Z= 0.260 Angle : 0.709 10.687 11211 Z= 0.353 Chirality : 0.050 0.429 1346 Planarity : 0.005 0.070 1418 Dihedral : 8.224 74.278 1501 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 5.68 % Allowed : 23.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.27), residues: 995 helix: 1.01 (0.42), residues: 169 sheet: -0.81 (0.30), residues: 314 loop : -2.41 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 395 HIS 0.006 0.001 HIS A 71 PHE 0.020 0.002 PHE B 418 TYR 0.027 0.002 TYR D 547 ARG 0.002 0.000 ARG B 474 *********************** 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 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 68 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6863 (tp40) cc_final: 0.5380 (mt0) REVERT: B 359 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6888 (mtm180) REVERT: B 599 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: C 67 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6756 (ppp) REVERT: D 506 GLN cc_start: 0.7705 (pm20) cc_final: 0.6774 (mm-40) outliers start: 49 outliers final: 37 residues processed: 108 average time/residue: 0.1603 time to fit residues: 25.2273 Evaluate side-chains 107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 68 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 578 GLU 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 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 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 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 41 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.203164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158542 restraints weight = 10711.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142331 restraints weight = 14592.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138323 restraints weight = 13038.794| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8225 Z= 0.190 Angle : 0.672 10.409 11211 Z= 0.331 Chirality : 0.047 0.352 1346 Planarity : 0.005 0.071 1418 Dihedral : 7.557 67.093 1501 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.29 % Allowed : 24.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.27), residues: 995 helix: 1.07 (0.42), residues: 169 sheet: -0.72 (0.30), residues: 316 loop : -2.33 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.012 0.001 PHE B 498 TYR 0.027 0.001 TYR D 547 ARG 0.005 0.000 ARG A 126 *********************** 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: 37 poor density : 75 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6674 (tp40) cc_final: 0.5336 (mt0) REVERT: C 67 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6772 (ppp) REVERT: D 469 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8429 (tt) outliers start: 37 outliers final: 29 residues processed: 101 average time/residue: 0.1838 time to fit residues: 26.4653 Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain 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 D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 415 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU 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 61 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 27 optimal weight: 0.0010 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.202093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169796 restraints weight = 10858.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162959 restraints weight = 26375.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157526 restraints weight = 14095.609| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8225 Z= 0.227 Angle : 0.691 9.248 11211 Z= 0.343 Chirality : 0.048 0.346 1346 Planarity : 0.005 0.070 1418 Dihedral : 7.206 62.269 1501 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 4.52 % Allowed : 24.71 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.27), residues: 995 helix: 1.12 (0.42), residues: 169 sheet: -0.69 (0.30), residues: 313 loop : -2.32 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 395 HIS 0.005 0.001 HIS A 71 PHE 0.013 0.001 PHE B 492 TYR 0.039 0.002 TYR D 547 ARG 0.005 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6608 (tp40) cc_final: 0.5280 (mt0) REVERT: C 67 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6667 (ppp) REVERT: C 165 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7262 (mt0) outliers start: 39 outliers final: 31 residues processed: 98 average time/residue: 0.1728 time to fit residues: 24.6383 Evaluate side-chains 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain 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 165 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU 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 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 76 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.202658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155845 restraints weight = 10909.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141305 restraints weight = 15687.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136877 restraints weight = 10857.546| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8225 Z= 0.214 Angle : 0.694 9.248 11211 Z= 0.343 Chirality : 0.047 0.385 1346 Planarity : 0.005 0.065 1418 Dihedral : 6.862 54.849 1501 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.29 % Allowed : 25.06 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.27), residues: 995 helix: 1.14 (0.42), residues: 169 sheet: -0.63 (0.30), residues: 313 loop : -2.31 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.012 0.001 PHE B 498 TYR 0.011 0.001 TYR D 600 ARG 0.005 0.000 ARG A 126 *********************** 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 109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6695 (tp40) cc_final: 0.5326 (mt0) REVERT: C 67 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6714 (ppp) REVERT: C 165 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7238 (mt0) outliers start: 37 outliers final: 31 residues processed: 100 average time/residue: 0.1691 time to fit residues: 24.4789 Evaluate side-chains 104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 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 572 GLU 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 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 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 589 THR Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 0.0570 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.203164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158338 restraints weight = 10738.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144934 restraints weight = 15906.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136270 restraints weight = 13759.626| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8225 Z= 0.200 Angle : 0.678 9.112 11211 Z= 0.336 Chirality : 0.047 0.410 1346 Planarity : 0.005 0.066 1418 Dihedral : 6.621 52.046 1501 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.06 % Allowed : 24.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 995 helix: 1.16 (0.42), residues: 169 sheet: -0.57 (0.30), residues: 313 loop : -2.29 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.012 0.001 PHE B 498 TYR 0.030 0.001 TYR D 547 ARG 0.004 0.000 ARG A 126 ********************** 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 108 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6666 (tp40) cc_final: 0.5305 (mt0) REVERT: B 254 PRO cc_start: 0.9277 (Cg_endo) cc_final: 0.9073 (Cg_exo) REVERT: B 359 ARG cc_start: 0.7187 (ptp-170) cc_final: 0.6532 (mtm180) REVERT: C 67 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: C 165 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7301 (mt0) outliers start: 35 outliers final: 32 residues processed: 99 average time/residue: 0.1777 time to fit residues: 25.7102 Evaluate side-chains 104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 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 572 GLU 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 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 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 502 MET Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.200598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154781 restraints weight = 10812.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141691 restraints weight = 16321.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135572 restraints weight = 10910.347| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8225 Z= 0.285 Angle : 0.719 9.028 11211 Z= 0.360 Chirality : 0.049 0.424 1346 Planarity : 0.005 0.065 1418 Dihedral : 6.416 52.023 1501 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.29 % Allowed : 24.83 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.27), residues: 995 helix: 1.20 (0.42), residues: 169 sheet: -0.62 (0.30), residues: 313 loop : -2.34 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 395 HIS 0.006 0.001 HIS A 71 PHE 0.014 0.002 PHE D 342 TYR 0.036 0.002 TYR D 547 ARG 0.007 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2729.25 seconds wall clock time: 49 minutes 44.61 seconds (2984.61 seconds total)