Starting phenix.real_space_refine on Sat Jul 26 02:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xt6_33440/07_2025/7xt6_33440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt6_33440/07_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_33440/07_2025/7xt6_33440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2025/7xt6_33440.map" model { file = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_2025/7xt6_33440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt6_33440/07_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-5711/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: 5.73, per 1000 atoms: 0.71 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: 2.27 Conformation dependent library (CDL) restraints added in 990.7 milliseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 24 sheets defined 19.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 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: 2.16 Time building geometry restraints manager: 2.65 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: 2.890 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.490 Find NCS groups from input model: 0.270 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8256 Z= 0.219 Angle : 0.861 13.377 11294 Z= 0.418 Chirality : 0.052 0.721 1346 Planarity : 0.005 0.079 1418 Dihedral : 17.764 109.282 3307 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.34 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 14) link_NAG-ASN : angle 4.17210 ( 42) link_BETA1-2 : bond 0.00374 ( 1) link_BETA1-2 : angle 0.69825 ( 3) link_BETA1-4 : bond 0.00743 ( 4) link_BETA1-4 : angle 3.39125 ( 12) link_ALPHA1-3 : bond 0.00254 ( 2) link_ALPHA1-3 : angle 1.91137 ( 6) hydrogen bonds : bond 0.23838 ( 240) hydrogen bonds : angle 8.28287 ( 672) SS BOND : bond 0.00571 ( 10) SS BOND : angle 1.40585 ( 20) covalent geometry : bond 0.00470 ( 8225) covalent geometry : angle 0.81446 (11211) *********************** 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 : 0.856 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: 0.2224 time to fit residues: 24.5618 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 : 0.905 ------------------------------------------------------------------------------- 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 = 78)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129564 restraints weight = 10874.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131712 restraints weight = 8229.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131715 restraints weight = 6785.346| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 8256 Z= 0.150 Angle : 0.759 12.444 11294 Z= 0.370 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 14) link_NAG-ASN : angle 3.62806 ( 42) link_BETA1-2 : bond 0.00816 ( 1) link_BETA1-2 : angle 1.57497 ( 3) link_BETA1-4 : bond 0.00477 ( 4) link_BETA1-4 : angle 3.22775 ( 12) link_ALPHA1-3 : bond 0.00997 ( 2) link_ALPHA1-3 : angle 2.61998 ( 6) hydrogen bonds : bond 0.05124 ( 240) hydrogen bonds : angle 6.41164 ( 672) SS BOND : bond 0.00769 ( 10) SS BOND : angle 1.52512 ( 20) covalent geometry : bond 0.00337 ( 8225) covalent geometry : angle 0.71555 (11211) *********************** 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 : 0.848 Fit side-chains revert: symmetry clash REVERT: B 454 ILE cc_start: 0.8205 (tp) cc_final: 0.7989 (pt) REVERT: B 578 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: C 67 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: D 469 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8584 (tt) REVERT: D 506 GLN cc_start: 0.7690 (pm20) cc_final: 0.6923 (mm-40) outliers start: 31 outliers final: 15 residues processed: 93 average time/residue: 0.1863 time to fit residues: 24.5504 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 : 0.915 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.194492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127566 restraints weight = 10950.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121750 restraints weight = 9000.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123619 restraints weight = 8386.336| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 8256 Z= 0.304 Angle : 0.880 11.857 11294 Z= 0.439 Chirality : 0.054 0.339 1346 Planarity : 0.006 0.067 1418 Dihedral : 10.495 93.006 1503 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 6.50 % Allowed : 23.09 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.27), residues: 995 helix: 0.70 (0.42), residues: 172 sheet: -1.15 (0.29), residues: 327 loop : -2.62 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 395 HIS 0.011 0.002 HIS A 71 PHE 0.019 0.002 PHE D 492 TYR 0.026 0.003 TYR D 547 ARG 0.005 0.001 ARG B 474 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 14) link_NAG-ASN : angle 3.55844 ( 42) link_BETA1-2 : bond 0.00646 ( 1) link_BETA1-2 : angle 2.23983 ( 3) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 3.50211 ( 12) link_ALPHA1-3 : bond 0.00973 ( 2) link_ALPHA1-3 : angle 2.78498 ( 6) hydrogen bonds : bond 0.06338 ( 240) hydrogen bonds : angle 6.26889 ( 672) SS BOND : bond 0.01138 ( 10) SS BOND : angle 2.46127 ( 20) covalent geometry : bond 0.00748 ( 8225) covalent geometry : angle 0.83840 (11211) *********************** 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 130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 74 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6900 (tp40) cc_final: 0.5270 (mt0) REVERT: A 126 ARG cc_start: 0.6757 (pmt-80) cc_final: 0.6505 (pmt-80) REVERT: B 359 ARG cc_start: 0.7425 (mtm180) cc_final: 0.6840 (mtm180) REVERT: B 470 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8681 (mt) REVERT: D 469 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8699 (tt) outliers start: 56 outliers final: 32 residues processed: 121 average time/residue: 0.1837 time to fit residues: 31.5556 Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 92 ILE 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 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: 0.6980 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.0020 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.197032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129302 restraints weight = 10880.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126740 restraints weight = 7463.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127804 restraints weight = 7092.096| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8256 Z= 0.138 Angle : 0.730 9.674 11294 Z= 0.355 Chirality : 0.048 0.334 1346 Planarity : 0.005 0.069 1418 Dihedral : 9.543 88.307 1503 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.22 % Allowed : 24.25 % 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: -2.07 (0.27), residues: 995 helix: 0.82 (0.42), residues: 169 sheet: -0.97 (0.29), residues: 326 loop : -2.51 (0.26), residues: 500 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 0.012 0.001 PHE B 498 TYR 0.026 0.001 TYR D 547 ARG 0.004 0.000 ARG B 474 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 14) link_NAG-ASN : angle 3.44314 ( 42) link_BETA1-2 : bond 0.00710 ( 1) link_BETA1-2 : angle 1.80264 ( 3) link_BETA1-4 : bond 0.00644 ( 4) link_BETA1-4 : angle 3.38714 ( 12) link_ALPHA1-3 : bond 0.00920 ( 2) link_ALPHA1-3 : angle 2.46432 ( 6) hydrogen bonds : bond 0.04742 ( 240) hydrogen bonds : angle 5.79495 ( 672) SS BOND : bond 0.00615 ( 10) SS BOND : angle 1.42562 ( 20) covalent geometry : bond 0.00305 ( 8225) covalent geometry : angle 0.68758 (11211) *********************** 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 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 68 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6809 (tp40) cc_final: 0.5418 (mt0) REVERT: B 599 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: C 67 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6687 (ppp) REVERT: D 469 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 45 outliers final: 30 residues processed: 102 average time/residue: 0.1866 time to fit residues: 27.5215 Evaluate side-chains 93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 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 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 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 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 454 ILE Chi-restraints excluded: chain D residue 469 LEU 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: 0.1980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 0.0070 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 = 0.203069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155098 restraints weight = 10709.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140993 restraints weight = 16363.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137365 restraints weight = 15714.121| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8256 Z= 0.126 Angle : 0.703 8.637 11294 Z= 0.340 Chirality : 0.047 0.355 1346 Planarity : 0.005 0.070 1418 Dihedral : 8.686 80.817 1503 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.52 % Allowed : 24.01 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.27), residues: 995 helix: 0.91 (0.41), residues: 169 sheet: -0.82 (0.29), residues: 337 loop : -2.46 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 395 HIS 0.004 0.001 HIS D 443 PHE 0.014 0.001 PHE B 418 TYR 0.025 0.001 TYR D 547 ARG 0.003 0.000 ARG B 474 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 14) link_NAG-ASN : angle 3.11182 ( 42) link_BETA1-2 : bond 0.00700 ( 1) link_BETA1-2 : angle 1.63462 ( 3) link_BETA1-4 : bond 0.00449 ( 4) link_BETA1-4 : angle 3.32492 ( 12) link_ALPHA1-3 : bond 0.00895 ( 2) link_ALPHA1-3 : angle 2.25905 ( 6) hydrogen bonds : bond 0.04322 ( 240) hydrogen bonds : angle 5.55036 ( 672) SS BOND : bond 0.00667 ( 10) SS BOND : angle 1.25034 ( 20) covalent geometry : bond 0.00277 ( 8225) covalent geometry : angle 0.66600 (11211) *********************** 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 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6646 (tp40) cc_final: 0.5320 (mt0) REVERT: B 359 ARG cc_start: 0.6957 (mtm180) cc_final: 0.6615 (mtm180) REVERT: C 67 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6753 (ppp) REVERT: C 162 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7009 (mp) outliers start: 39 outliers final: 27 residues processed: 94 average time/residue: 0.1719 time to fit residues: 23.4225 Evaluate side-chains 92 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 GLU 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 578 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 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 589 THR Chi-restraints excluded: chain D residue 598 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.199960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151157 restraints weight = 10694.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130384 restraints weight = 15156.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133219 restraints weight = 13462.043| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8256 Z= 0.181 Angle : 0.760 9.627 11294 Z= 0.369 Chirality : 0.051 0.466 1346 Planarity : 0.005 0.071 1418 Dihedral : 8.190 74.445 1501 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.57 % Allowed : 23.09 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.27), residues: 995 helix: 1.03 (0.42), residues: 169 sheet: -0.88 (0.30), residues: 311 loop : -2.40 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 395 HIS 0.007 0.001 HIS A 71 PHE 0.013 0.002 PHE B 492 TYR 0.028 0.002 TYR D 547 ARG 0.003 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 14) link_NAG-ASN : angle 3.24714 ( 42) link_BETA1-2 : bond 0.00698 ( 1) link_BETA1-2 : angle 1.91573 ( 3) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 3.45491 ( 12) link_ALPHA1-3 : bond 0.00739 ( 2) link_ALPHA1-3 : angle 2.52573 ( 6) hydrogen bonds : bond 0.04834 ( 240) hydrogen bonds : angle 5.58539 ( 672) SS BOND : bond 0.00888 ( 10) SS BOND : angle 1.88929 ( 20) covalent geometry : bond 0.00430 ( 8225) covalent geometry : angle 0.72041 (11211) *********************** 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 114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 66 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6823 (tp40) cc_final: 0.5358 (mt0) REVERT: C 162 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7122 (mp) REVERT: D 415 ASN cc_start: 0.5296 (OUTLIER) cc_final: 0.5086 (m110) REVERT: D 469 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8433 (tp) REVERT: D 506 GLN cc_start: 0.7860 (pm20) cc_final: 0.7152 (mm-40) outliers start: 48 outliers final: 34 residues processed: 108 average time/residue: 0.1641 time to fit residues: 25.9933 Evaluate side-chains 104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.201790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155506 restraints weight = 10726.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144664 restraints weight = 16849.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137635 restraints weight = 11797.837| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8256 Z= 0.140 Angle : 0.721 10.784 11294 Z= 0.347 Chirality : 0.048 0.353 1346 Planarity : 0.005 0.070 1418 Dihedral : 7.625 67.996 1501 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.99 % Allowed : 23.78 % 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: -1.81 (0.27), residues: 995 helix: 1.05 (0.42), residues: 169 sheet: -0.79 (0.30), residues: 316 loop : -2.34 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.017 0.001 PHE B 418 TYR 0.027 0.001 TYR D 547 ARG 0.002 0.000 ARG B 474 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 14) link_NAG-ASN : angle 2.97292 ( 42) link_BETA1-2 : bond 0.00757 ( 1) link_BETA1-2 : angle 1.80637 ( 3) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 3.37749 ( 12) link_ALPHA1-3 : bond 0.00792 ( 2) link_ALPHA1-3 : angle 2.30127 ( 6) hydrogen bonds : bond 0.04321 ( 240) hydrogen bonds : angle 5.43522 ( 672) SS BOND : bond 0.00630 ( 10) SS BOND : angle 1.40850 ( 20) covalent geometry : bond 0.00320 ( 8225) covalent geometry : angle 0.68669 (11211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6661 (tp40) cc_final: 0.5285 (mt0) REVERT: B 359 ARG cc_start: 0.6956 (mtm180) cc_final: 0.6736 (mtm180) REVERT: B 599 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: C 67 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6736 (ppp) REVERT: C 162 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7139 (mt) REVERT: D 415 ASN cc_start: 0.5298 (OUTLIER) cc_final: 0.5083 (m110) outliers start: 43 outliers final: 34 residues processed: 102 average time/residue: 0.1668 time to fit residues: 24.8581 Evaluate side-chains 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 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 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 C residue 162 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 8 optimal weight: 0.0170 chunk 27 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.202819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153989 restraints weight = 10872.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138093 restraints weight = 15301.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137731 restraints weight = 11395.115| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8256 Z= 0.130 Angle : 0.706 9.427 11294 Z= 0.341 Chirality : 0.047 0.348 1346 Planarity : 0.005 0.069 1418 Dihedral : 7.116 61.975 1501 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 5.34 % Allowed : 23.55 % Favored : 71.11 % 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: -1.73 (0.27), residues: 995 helix: 1.12 (0.42), residues: 169 sheet: -0.74 (0.30), residues: 313 loop : -2.28 (0.26), residues: 513 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 0.028 0.001 TYR D 547 ARG 0.005 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 14) link_NAG-ASN : angle 2.79633 ( 42) link_BETA1-2 : bond 0.00754 ( 1) link_BETA1-2 : angle 1.76519 ( 3) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 3.34672 ( 12) link_ALPHA1-3 : bond 0.00780 ( 2) link_ALPHA1-3 : angle 2.26532 ( 6) hydrogen bonds : bond 0.04107 ( 240) hydrogen bonds : angle 5.31001 ( 672) SS BOND : bond 0.00654 ( 10) SS BOND : angle 1.32931 ( 20) covalent geometry : bond 0.00290 ( 8225) covalent geometry : angle 0.67399 (11211) *********************** 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 115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 69 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6695 (tp40) cc_final: 0.5312 (mt0) REVERT: B 593 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7030 (tp) REVERT: C 67 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6751 (ppp) REVERT: C 165 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7244 (mt0) outliers start: 46 outliers final: 35 residues processed: 106 average time/residue: 0.1779 time to fit residues: 26.9927 Evaluate side-chains 105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 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 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 591 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 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 460 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.0470 chunk 10 optimal weight: 0.0970 chunk 76 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.205009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168227 restraints weight = 10928.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168764 restraints weight = 25718.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165383 restraints weight = 10889.614| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8256 Z= 0.119 Angle : 0.691 9.554 11294 Z= 0.333 Chirality : 0.047 0.356 1346 Planarity : 0.005 0.069 1418 Dihedral : 6.621 53.354 1501 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.94 % Allowed : 24.48 % Favored : 71.58 % 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: -1.62 (0.27), residues: 995 helix: 1.12 (0.41), residues: 169 sheet: -0.59 (0.30), residues: 313 loop : -2.22 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 395 HIS 0.003 0.001 HIS D 443 PHE 0.016 0.001 PHE D 342 TYR 0.038 0.001 TYR D 547 ARG 0.005 0.000 ARG B 359 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 14) link_NAG-ASN : angle 2.65515 ( 42) link_BETA1-2 : bond 0.00698 ( 1) link_BETA1-2 : angle 1.59920 ( 3) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 3.21486 ( 12) link_ALPHA1-3 : bond 0.00803 ( 2) link_ALPHA1-3 : angle 2.03974 ( 6) hydrogen bonds : bond 0.03803 ( 240) hydrogen bonds : angle 5.15061 ( 672) SS BOND : bond 0.00496 ( 10) SS BOND : angle 1.13372 ( 20) covalent geometry : bond 0.00253 ( 8225) covalent geometry : angle 0.66169 (11211) *********************** 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 105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6503 (tp40) cc_final: 0.5207 (mt0) REVERT: C 67 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6782 (ppp) REVERT: C 165 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: D 415 ASN cc_start: 0.4532 (OUTLIER) cc_final: 0.4187 (m110) outliers start: 34 outliers final: 29 residues processed: 97 average time/residue: 0.2218 time to fit residues: 31.9797 Evaluate side-chains 100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 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 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 415 ASN 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 605 THR Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.201791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155518 restraints weight = 10783.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141562 restraints weight = 16088.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135678 restraints weight = 10326.946| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8256 Z= 0.168 Angle : 0.741 9.393 11294 Z= 0.362 Chirality : 0.049 0.390 1346 Planarity : 0.005 0.067 1418 Dihedral : 6.525 52.358 1501 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 3.83 % Allowed : 24.36 % Favored : 71.81 % 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: -1.63 (0.27), residues: 995 helix: 1.22 (0.42), residues: 169 sheet: -0.62 (0.30), residues: 313 loop : -2.27 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 395 HIS 0.005 0.001 HIS A 71 PHE 0.016 0.002 PHE D 342 TYR 0.010 0.001 TYR B 513 ARG 0.004 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 14) link_NAG-ASN : angle 2.69739 ( 42) link_BETA1-2 : bond 0.00637 ( 1) link_BETA1-2 : angle 1.95032 ( 3) link_BETA1-4 : bond 0.00313 ( 4) link_BETA1-4 : angle 3.27514 ( 12) link_ALPHA1-3 : bond 0.00844 ( 2) link_ALPHA1-3 : angle 2.46841 ( 6) hydrogen bonds : bond 0.04401 ( 240) hydrogen bonds : angle 5.30772 ( 672) SS BOND : bond 0.00818 ( 10) SS BOND : angle 1.72143 ( 20) covalent geometry : bond 0.00396 ( 8225) covalent geometry : angle 0.71077 (11211) ********************** 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 99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6699 (tp40) cc_final: 0.5276 (mt0) REVERT: C 67 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6760 (ppp) REVERT: C 165 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: D 415 ASN cc_start: 0.5427 (OUTLIER) cc_final: 0.5164 (m110) outliers start: 33 outliers final: 29 residues processed: 92 average time/residue: 0.1618 time to fit residues: 21.9651 Evaluate side-chains 97 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU 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 415 ASN 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 605 THR Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.203025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.157868 restraints weight = 10847.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144797 restraints weight = 16487.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136743 restraints weight = 11025.724| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8256 Z= 0.136 Angle : 0.703 8.623 11294 Z= 0.344 Chirality : 0.047 0.377 1346 Planarity : 0.005 0.088 1418 Dihedral : 6.276 52.493 1501 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.18 % Allowed : 24.13 % Favored : 71.69 % 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: -1.60 (0.27), residues: 995 helix: 1.17 (0.42), residues: 169 sheet: -0.59 (0.30), residues: 313 loop : -2.22 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.015 0.001 PHE B 418 TYR 0.013 0.001 TYR D 600 ARG 0.004 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 14) link_NAG-ASN : angle 2.54038 ( 42) link_BETA1-2 : bond 0.00653 ( 1) link_BETA1-2 : angle 1.83772 ( 3) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 3.10467 ( 12) link_ALPHA1-3 : bond 0.00711 ( 2) link_ALPHA1-3 : angle 2.23066 ( 6) hydrogen bonds : bond 0.04046 ( 240) hydrogen bonds : angle 5.25644 ( 672) SS BOND : bond 0.00626 ( 10) SS BOND : angle 1.41375 ( 20) covalent geometry : bond 0.00311 ( 8225) covalent geometry : angle 0.67517 (11211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.52 seconds wall clock time: 54 minutes 48.00 seconds (3288.00 seconds total)