Starting phenix.real_space_refine on Thu Jul 2 23:35:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.cif Found real_map, /net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.cif" model { file = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7drc_30826/07_2026/7drc_30826.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 42 5.16 5 C 6797 2.51 5 N 1727 2.21 5 O 2171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10737 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "C" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7114 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 39, 'TRANS': 866} Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1360 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.86, per 1000 atoms: 0.27 Number of scatterers: 10737 At special positions: 0 Unit cell: (127.32, 98.673, 128.381, 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 42 16.00 O 2171 8.00 N 1727 7.00 C 6797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " distance=2.02 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 67 " distance=2.03 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 ALPHA1-2 " MAN F 5 " - " MAN F 6 " ALPHA1-3 " BMA F 3 " - " MAN F 8 " " MAN F 4 " - " MAN F 7 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B1000 " - " ASN B 82 " " NAG B1001 " - " ASN B 106 " " NAG B1002 " - " ASN B 117 " " NAG B1003 " - " ASN B 152 " " NAG C1001 " - " ASN C 159 " " NAG C1002 " - " ASN C 234 " " NAG C1003 " - " ASN C 261 " " NAG C1004 " - " ASN C 532 " " NAG C1005 " - " ASN C 542 " " NAG C1006 " - " ASN C 591 " " NAG C1007 " - " ASN C 660 " " NAG C1008 " - " ASN C 855 " " NAG C1009 " - " ASN C 888 " " NAG D 1 " - " ASN B 186 " " NAG E 1 " - " ASN C 73 " " NAG F 1 " - " ASN C 143 " " NAG G 1 " - " ASN C 311 " " NAG H 1 " - " ASN C 481 " " NAG I 1 " - " ASN C 562 " " NAG J 1 " - " ASN C 647 " " NAG K 1 " - " ASN C 767 " " NAG L 1 " - " ASN C 848 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 403.1 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 18.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.565A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.824A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.787A pdb=" N ILE C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.607A pdb=" N PHE C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 340 removed outlier: 3.954A pdb=" N ARG C 340 " --> pdb=" O SER C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 340' Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.836A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.697A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 456 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 457 " --> pdb=" O MET C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 457' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.722A pdb=" N CYS C 621 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 672 Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.773A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.641A pdb=" N LEU C 744 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 745 " --> pdb=" O CYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 768 removed outlier: 3.526A pdb=" N PHE C 768 " --> pdb=" O PHE C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 839 removed outlier: 3.670A pdb=" N MET C 838 " --> pdb=" O PRO C 835 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 839 " --> pdb=" O LYS C 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 835 through 839' Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 883 through 889 removed outlier: 3.514A pdb=" N LEU C 889 " --> pdb=" O LEU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 915 removed outlier: 3.509A pdb=" N PHE C 915 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.519A pdb=" N ASN B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 4.123A pdb=" N GLY B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.700A pdb=" N LEU B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.607A pdb=" N THR B 164 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.646A pdb=" N PHE B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 191 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 192 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.574A pdb=" N VAL A 36 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 59 removed outlier: 4.782A pdb=" N SER A 48 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 72 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 64 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 58 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 63 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 235 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 65 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP A 71 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 227 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS A 105 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 236 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 103 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 238 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.674A pdb=" N ALA A 158 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 142 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 119 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA A 143 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 117 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP A 118 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 221 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 120 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 219 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP A 122 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 217 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 124 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.679A pdb=" N GLU C 71 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 80 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP C 118 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 117 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 318 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 416 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 440 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.367A pdb=" N GLY C 151 " --> pdb=" O ILE C 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.548A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 424 through 426 removed outlier: 7.070A pdb=" N GLY C 425 " --> pdb=" O GLU C 448 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 471 through 474 removed outlier: 4.483A pdb=" N GLY C 472 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 487 through 489 removed outlier: 6.331A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 512 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU C 630 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 678 " --> pdb=" O ASP C 702 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 701 " --> pdb=" O SER C 727 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 726 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 750 " --> pdb=" O ASP C 824 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 823 " --> pdb=" O ASN C 848 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 847 " --> pdb=" O ASP C 872 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 569 through 570 removed outlier: 5.582A pdb=" N GLY C 570 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE C 592 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 614 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY C 594 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE C 613 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 638 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU C 640 " --> pdb=" O GLY C 615 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE C 637 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 662 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C 639 " --> pdb=" O SER C 662 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE C 661 " --> pdb=" O SER C 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 782 through 789 removed outlier: 3.931A pdb=" N GLY C 787 " --> pdb=" O TYR C 792 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C 792 " --> pdb=" O GLY C 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 802 through 806 Processing sheet with id=AB5, first strand: chain 'C' and resid 831 through 832 removed outlier: 5.508A pdb=" N GLY C 832 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU C 854 " --> pdb=" O GLN C 877 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 903 through 904 removed outlier: 4.174A pdb=" N GLY C 904 " --> pdb=" O GLN C 925 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.618A pdb=" N ARG B 75 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 76 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 125 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 148 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 185 hydrogen bonds defined for protein. 360 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: 2.50 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3355 1.35 - 1.47: 2742 1.47 - 1.59: 4791 1.59 - 1.72: 0 1.72 - 1.84: 62 Bond restraints: 10950 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.20e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 ... (remaining 10945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14317 1.72 - 3.44: 442 3.44 - 5.16: 81 5.16 - 6.88: 24 6.88 - 8.60: 2 Bond angle restraints: 14866 Sorted by residual: angle pdb=" C3 MAN F 5 " pdb=" C2 MAN F 5 " pdb=" O2 MAN F 5 " ideal model delta sigma weight residual 111.77 104.34 7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" CA LEU C 931 " pdb=" CB LEU C 931 " pdb=" CG LEU C 931 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.04e+00 angle pdb=" CA GLU C 123 " pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " ideal model delta sigma weight residual 114.10 118.95 -4.85 2.00e+00 2.50e-01 5.88e+00 angle pdb=" CA MET A 138 " pdb=" CB MET A 138 " pdb=" CG MET A 138 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C ILE A 137 " pdb=" N MET A 138 " pdb=" CA MET A 138 " ideal model delta sigma weight residual 121.42 124.73 -3.31 1.43e+00 4.89e-01 5.37e+00 ... (remaining 14861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5652 17.99 - 35.97: 485 35.97 - 53.96: 65 53.96 - 71.95: 10 71.95 - 89.93: 3 Dihedral angle restraints: 6215 sinusoidal: 2450 harmonic: 3765 Sorted by residual: dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual 93.00 40.58 52.42 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS C 621 " pdb=" SG CYS C 621 " pdb=" SG CYS C 644 " pdb=" CB CYS C 644 " ideal model delta sinusoidal sigma weight residual -86.00 -39.45 -46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA PHE C 284 " pdb=" C PHE C 284 " pdb=" N GLY C 285 " pdb=" CA GLY C 285 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1631 0.083 - 0.165: 183 0.165 - 0.248: 8 0.248 - 0.331: 7 0.331 - 0.414: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 767 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1827 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 929 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 930 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 930 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 930 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 106 " 0.020 2.00e-02 2.50e+03 1.81e-02 4.11e+00 pdb=" CG ASN B 106 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 106 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 106 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B1001 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 767 " 0.018 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN C 767 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 767 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 767 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.021 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1193 2.75 - 3.29: 10520 3.29 - 3.82: 16912 3.82 - 4.36: 21161 4.36 - 4.90: 35712 Nonbonded interactions: 85498 Sorted by model distance: nonbonded pdb=" NE2 GLN C 372 " pdb=" OD2 ASP C 394 " model vdw 2.211 3.120 nonbonded pdb=" O ASN C 468 " pdb=" ND2 ASN C 493 " model vdw 2.267 3.120 nonbonded pdb=" OE1 GLU A 136 " pdb=" OH TYR C 792 " model vdw 2.272 3.040 nonbonded pdb=" NE2 GLN C 911 " pdb=" OD1 ASP B 77 " model vdw 2.276 3.120 nonbonded pdb=" ND2 ASN A 84 " pdb=" OE1 GLU A 218 " model vdw 2.297 3.120 ... (remaining 85493 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 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.057 11000 Z= 0.218 Angle : 0.762 8.953 15011 Z= 0.346 Chirality : 0.053 0.414 1830 Planarity : 0.004 0.078 1838 Dihedral : 12.991 89.931 3776 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.22), residues: 1298 helix: -2.70 (0.32), residues: 203 sheet: -2.74 (0.30), residues: 275 loop : -1.41 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 571 TYR 0.025 0.002 TYR A 108 PHE 0.016 0.001 PHE A 224 TRP 0.011 0.001 TRP B 62 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (10950) covalent geometry : angle 0.73642 / 0.34 (14866) SS BOND : bond 0.00460 / 0.24 ( 5) SS BOND : angle 2.38221 / 1.74 ( 10) hydrogen bonds : bond 0.21058 / 13.80 ( 185) hydrogen bonds : angle 6.98588 / 4.91 ( 360) link_ALPHA1-2 : bond 0.00221 / 0.14 ( 1) link_ALPHA1-2 : angle 2.60071 / 1.44 ( 3) link_ALPHA1-3 : bond 0.00404 / 0.23 ( 3) link_ALPHA1-3 : angle 1.61240 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00210 / 0.11 ( 3) link_ALPHA1-6 : angle 2.11860 / 1.21 ( 9) link_BETA1-4 : bond 0.00507 / 0.34 ( 16) link_BETA1-4 : angle 1.52758 / 0.90 ( 48) link_NAG-ASN : bond 0.00384 / 0.25 ( 22) link_NAG-ASN : angle 2.45317 / 1.57 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8272 (p90) cc_final: 0.7636 (p90) REVERT: A 138 MET cc_start: 0.7923 (mmt) cc_final: 0.7696 (mmp) REVERT: C 59 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7136 (mm-30) REVERT: C 103 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7826 (ttmm) REVERT: C 123 GLU cc_start: 0.7235 (pp20) cc_final: 0.6925 (pp20) REVERT: C 353 MET cc_start: 0.7981 (mtp) cc_final: 0.7755 (mtm) REVERT: C 498 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7626 (ttmt) REVERT: C 544 SER cc_start: 0.8172 (p) cc_final: 0.7883 (p) REVERT: C 781 MET cc_start: 0.8037 (ttm) cc_final: 0.7663 (ttp) REVERT: C 813 TYR cc_start: 0.7879 (t80) cc_final: 0.7595 (t80) REVERT: C 831 VAL cc_start: 0.8207 (t) cc_final: 0.7969 (p) REVERT: C 881 MET cc_start: 0.7455 (ptp) cc_final: 0.7201 (ptp) REVERT: C 932 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7691 (mm-40) REVERT: B 105 ASN cc_start: 0.7697 (m-40) cc_final: 0.7205 (m-40) REVERT: B 123 SER cc_start: 0.8755 (t) cc_final: 0.8545 (t) REVERT: B 139 LEU cc_start: 0.8543 (tt) cc_final: 0.8201 (tp) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.4912 time to fit residues: 160.8863 Evaluate side-chains 277 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN C 279 GLN C 322 ASN C 456 GLN C 805 GLN C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 178 ASN B 199 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094693 restraints weight = 16493.679| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.39 r_work: 0.3111 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11000 Z= 0.206 Angle : 0.678 12.760 15011 Z= 0.328 Chirality : 0.049 0.268 1830 Planarity : 0.005 0.055 1838 Dihedral : 5.043 19.676 1378 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.30 % Allowed : 12.45 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.22), residues: 1298 helix: -2.68 (0.32), residues: 205 sheet: -2.75 (0.29), residues: 292 loop : -1.35 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 917 TYR 0.020 0.002 TYR C 533 PHE 0.022 0.002 PHE A 224 TRP 0.009 0.001 TRP A 28 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (10950) covalent geometry : angle 0.65758 / 0.32 (14866) SS BOND : bond 0.00655 / 0.41 ( 5) SS BOND : angle 2.16147 / 1.39 ( 10) hydrogen bonds : bond 0.04468 / 2.90 ( 185) hydrogen bonds : angle 5.57112 / 3.93 ( 360) link_ALPHA1-2 : bond 0.00387 / 0.24 ( 1) link_ALPHA1-2 : angle 2.01320 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00609 / 0.36 ( 3) link_ALPHA1-3 : angle 1.45675 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00183 / 0.09 ( 3) link_ALPHA1-6 : angle 1.60576 / 1.07 ( 9) link_BETA1-4 : bond 0.00493 / 0.32 ( 16) link_BETA1-4 : angle 1.61354 / 1.02 ( 48) link_NAG-ASN : bond 0.00599 / 0.43 ( 22) link_NAG-ASN : angle 1.91974 / 1.29 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8951 (m-80) cc_final: 0.8724 (m-80) REVERT: A 66 HIS cc_start: 0.8643 (p90) cc_final: 0.7870 (p90) REVERT: C 103 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8117 (ttmm) REVERT: C 123 GLU cc_start: 0.7840 (pp20) cc_final: 0.7420 (pp20) REVERT: C 189 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7749 (tp) REVERT: C 300 ASN cc_start: 0.8477 (t0) cc_final: 0.8271 (t0) REVERT: C 498 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8019 (ttmt) REVERT: C 610 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8198 (ttpt) REVERT: C 707 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8247 (mtpt) REVERT: C 711 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7978 (ttm-80) REVERT: C 764 CYS cc_start: 0.7073 (p) cc_final: 0.6771 (p) REVERT: C 781 MET cc_start: 0.8481 (ttm) cc_final: 0.8056 (ttp) REVERT: C 813 TYR cc_start: 0.8013 (t80) cc_final: 0.7765 (t80) REVERT: C 881 MET cc_start: 0.8495 (ptp) cc_final: 0.8239 (ptp) REVERT: C 932 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8054 (mm-40) REVERT: B 139 LEU cc_start: 0.8655 (tt) cc_final: 0.8390 (tp) outliers start: 15 outliers final: 8 residues processed: 290 average time/residue: 0.4841 time to fit residues: 152.6261 Evaluate side-chains 283 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 274 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 GLN C 456 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 GLN C 923 ASN B 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094595 restraints weight = 16417.281| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.41 r_work: 0.3113 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11000 Z= 0.180 Angle : 0.652 11.427 15011 Z= 0.313 Chirality : 0.048 0.279 1830 Planarity : 0.004 0.057 1838 Dihedral : 4.967 19.425 1378 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.33 % Allowed : 14.52 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.22), residues: 1298 helix: -2.66 (0.32), residues: 211 sheet: -2.76 (0.28), residues: 303 loop : -1.30 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 917 TYR 0.018 0.002 TYR C 533 PHE 0.022 0.002 PHE A 224 TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10950) covalent geometry : angle 0.63277 / 0.31 (14866) SS BOND : bond 0.00506 / 0.27 ( 5) SS BOND : angle 1.72249 / 0.99 ( 10) hydrogen bonds : bond 0.03713 / 2.41 ( 185) hydrogen bonds : angle 5.40005 / 3.78 ( 360) link_ALPHA1-2 : bond 0.00175 / 0.11 ( 1) link_ALPHA1-2 : angle 1.95762 / 1.04 ( 3) link_ALPHA1-3 : bond 0.00660 / 0.38 ( 3) link_ALPHA1-3 : angle 1.35448 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00230 / 0.12 ( 3) link_ALPHA1-6 : angle 1.58714 / 0.99 ( 9) link_BETA1-4 : bond 0.00492 / 0.32 ( 16) link_BETA1-4 : angle 1.53504 / 0.95 ( 48) link_NAG-ASN : bond 0.00563 / 0.39 ( 22) link_NAG-ASN : angle 1.90412 / 1.33 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8976 (m-80) cc_final: 0.8701 (m-80) REVERT: A 66 HIS cc_start: 0.8655 (p90) cc_final: 0.7938 (p90) REVERT: C 74 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8404 (mmmm) REVERT: C 83 ASP cc_start: 0.8377 (p0) cc_final: 0.8085 (p0) REVERT: C 103 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8281 (tttm) REVERT: C 123 GLU cc_start: 0.7908 (pp20) cc_final: 0.7451 (pp20) REVERT: C 189 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7827 (tp) REVERT: C 300 ASN cc_start: 0.8458 (t0) cc_final: 0.8208 (t0) REVERT: C 498 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7983 (ttmt) REVERT: C 544 SER cc_start: 0.8390 (p) cc_final: 0.7975 (p) REVERT: C 610 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8185 (ttpt) REVERT: C 707 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8235 (mtpt) REVERT: C 711 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8014 (ttm-80) REVERT: C 781 MET cc_start: 0.8488 (ttm) cc_final: 0.8139 (ttp) REVERT: C 881 MET cc_start: 0.8516 (ptp) cc_final: 0.8293 (ptp) REVERT: B 139 LEU cc_start: 0.8669 (tt) cc_final: 0.8385 (tp) outliers start: 27 outliers final: 16 residues processed: 282 average time/residue: 0.4763 time to fit residues: 146.5178 Evaluate side-chains 298 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 280 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 113 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN C 279 GLN C 456 GLN C 877 GLN C 911 GLN C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095740 restraints weight = 16431.580| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.41 r_work: 0.3127 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11000 Z= 0.121 Angle : 0.635 15.739 15011 Z= 0.301 Chirality : 0.047 0.338 1830 Planarity : 0.004 0.061 1838 Dihedral : 4.788 19.143 1378 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.77 % Allowed : 15.73 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1298 helix: -2.64 (0.32), residues: 211 sheet: -2.75 (0.28), residues: 308 loop : -1.25 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 917 TYR 0.016 0.001 TYR C 533 PHE 0.016 0.001 PHE A 224 TRP 0.007 0.001 TRP A 65 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10950) covalent geometry : angle 0.60279 / 0.29 (14866) SS BOND : bond 0.00453 / 0.23 ( 5) SS BOND : angle 1.43714 / 0.81 ( 10) hydrogen bonds : bond 0.03133 / 2.00 ( 185) hydrogen bonds : angle 5.24567 / 3.67 ( 360) link_ALPHA1-2 : bond 0.00246 / 0.15 ( 1) link_ALPHA1-2 : angle 1.89791 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00616 / 0.36 ( 3) link_ALPHA1-3 : angle 1.36692 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00277 / 0.15 ( 3) link_ALPHA1-6 : angle 1.54860 / 0.98 ( 9) link_BETA1-4 : bond 0.00493 / 0.32 ( 16) link_BETA1-4 : angle 1.42927 / 0.90 ( 48) link_NAG-ASN : bond 0.00489 / 0.35 ( 22) link_NAG-ASN : angle 2.72434 / 2.28 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8953 (m-80) cc_final: 0.8703 (m-80) REVERT: A 66 HIS cc_start: 0.8625 (p90) cc_final: 0.7912 (p90) REVERT: C 74 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8374 (mmmm) REVERT: C 83 ASP cc_start: 0.8322 (p0) cc_final: 0.8042 (p0) REVERT: C 103 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8171 (ttmm) REVERT: C 123 GLU cc_start: 0.7915 (pp20) cc_final: 0.7448 (pp20) REVERT: C 187 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 189 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7677 (tp) REVERT: C 300 ASN cc_start: 0.8462 (t0) cc_final: 0.8231 (t0) REVERT: C 498 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7961 (ttmt) REVERT: C 544 SER cc_start: 0.8404 (p) cc_final: 0.8008 (p) REVERT: C 674 ASN cc_start: 0.8227 (m110) cc_final: 0.7877 (m-40) REVERT: C 707 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8210 (mtpt) REVERT: C 711 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: C 781 MET cc_start: 0.8457 (ttm) cc_final: 0.8130 (ttp) REVERT: C 881 MET cc_start: 0.8512 (ptp) cc_final: 0.8297 (ptp) outliers start: 32 outliers final: 16 residues processed: 289 average time/residue: 0.4463 time to fit residues: 141.1120 Evaluate side-chains 291 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 GLN C 456 GLN C 877 GLN C 911 GLN C 923 ASN B 36 ASN B 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094359 restraints weight = 16358.900| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.37 r_work: 0.3106 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11000 Z= 0.223 Angle : 0.689 11.826 15011 Z= 0.330 Chirality : 0.049 0.292 1830 Planarity : 0.004 0.069 1838 Dihedral : 4.996 19.198 1378 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.03 % Allowed : 16.68 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.22), residues: 1298 helix: -2.77 (0.31), residues: 217 sheet: -2.80 (0.28), residues: 299 loop : -1.30 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 917 TYR 0.019 0.002 TYR C 533 PHE 0.025 0.002 PHE A 224 TRP 0.010 0.001 TRP A 28 HIS 0.006 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (10950) covalent geometry : angle 0.66519 / 0.32 (14866) SS BOND : bond 0.00694 / 0.37 ( 5) SS BOND : angle 2.55311 / 1.47 ( 10) hydrogen bonds : bond 0.03628 / 2.34 ( 185) hydrogen bonds : angle 5.37694 / 3.74 ( 360) link_ALPHA1-2 : bond 0.00253 / 0.16 ( 1) link_ALPHA1-2 : angle 1.89087 / 0.99 ( 3) link_ALPHA1-3 : bond 0.00591 / 0.34 ( 3) link_ALPHA1-3 : angle 1.36268 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00164 / 0.08 ( 3) link_ALPHA1-6 : angle 1.58494 / 0.99 ( 9) link_BETA1-4 : bond 0.00484 / 0.31 ( 16) link_BETA1-4 : angle 1.50894 / 0.92 ( 48) link_NAG-ASN : bond 0.00440 / 0.30 ( 22) link_NAG-ASN : angle 2.24596 / 1.65 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8978 (m-80) cc_final: 0.8673 (m-80) REVERT: C 74 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8376 (mmmm) REVERT: C 83 ASP cc_start: 0.8323 (p0) cc_final: 0.8000 (p0) REVERT: C 103 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8325 (tttm) REVERT: C 123 GLU cc_start: 0.7919 (pp20) cc_final: 0.7409 (pp20) REVERT: C 189 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7856 (tp) REVERT: C 300 ASN cc_start: 0.8461 (t0) cc_final: 0.8202 (t0) REVERT: C 498 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8001 (ttmt) REVERT: C 544 SER cc_start: 0.8380 (p) cc_final: 0.7968 (p) REVERT: C 545 ASP cc_start: 0.7956 (t0) cc_final: 0.7696 (t0) REVERT: C 646 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8515 (pmm) REVERT: C 660 ASN cc_start: 0.7421 (t0) cc_final: 0.7190 (t0) REVERT: C 674 ASN cc_start: 0.8224 (m110) cc_final: 0.7917 (m-40) REVERT: C 707 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8207 (mtpt) REVERT: C 711 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8052 (ttm-80) REVERT: C 781 MET cc_start: 0.8521 (ttm) cc_final: 0.8223 (ttp) REVERT: C 831 VAL cc_start: 0.8501 (p) cc_final: 0.8275 (t) REVERT: C 881 MET cc_start: 0.8530 (ptp) cc_final: 0.8320 (ptp) outliers start: 35 outliers final: 20 residues processed: 292 average time/residue: 0.4461 time to fit residues: 142.3441 Evaluate side-chains 293 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 271 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 646 MET Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN C 279 GLN C 456 GLN C 612 GLN C 801 ASN C 809 GLN C 877 GLN C 911 GLN C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 178 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095786 restraints weight = 16446.762| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.38 r_work: 0.3129 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11000 Z= 0.130 Angle : 0.643 10.300 15011 Z= 0.309 Chirality : 0.047 0.442 1830 Planarity : 0.004 0.070 1838 Dihedral : 4.793 18.809 1378 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.33 % Allowed : 17.89 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.22), residues: 1298 helix: -2.78 (0.31), residues: 218 sheet: -2.80 (0.28), residues: 304 loop : -1.26 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 917 TYR 0.016 0.001 TYR C 533 PHE 0.016 0.001 PHE A 224 TRP 0.007 0.001 TRP A 65 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10950) covalent geometry : angle 0.61994 / 0.30 (14866) SS BOND : bond 0.00785 / 0.43 ( 5) SS BOND : angle 2.61632 / 1.46 ( 10) hydrogen bonds : bond 0.03032 / 1.93 ( 185) hydrogen bonds : angle 5.20673 / 3.63 ( 360) link_ALPHA1-2 : bond 0.00176 / 0.11 ( 1) link_ALPHA1-2 : angle 1.83838 / 0.98 ( 3) link_ALPHA1-3 : bond 0.00577 / 0.33 ( 3) link_ALPHA1-3 : angle 1.37959 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00256 / 0.14 ( 3) link_ALPHA1-6 : angle 1.53431 / 0.97 ( 9) link_BETA1-4 : bond 0.00493 / 0.32 ( 16) link_BETA1-4 : angle 1.38087 / 0.86 ( 48) link_NAG-ASN : bond 0.00359 / 0.22 ( 22) link_NAG-ASN : angle 2.04105 / 1.43 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8965 (m-80) cc_final: 0.8695 (m-80) REVERT: A 66 HIS cc_start: 0.8638 (p90) cc_final: 0.7963 (p90) REVERT: A 69 TYR cc_start: 0.8908 (p90) cc_final: 0.8557 (p90) REVERT: A 122 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8254 (t0) REVERT: C 74 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8342 (mmmm) REVERT: C 83 ASP cc_start: 0.8298 (p0) cc_final: 0.8004 (p0) REVERT: C 103 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8177 (ttmm) REVERT: C 123 GLU cc_start: 0.7910 (pp20) cc_final: 0.7417 (pp20) REVERT: C 189 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7661 (tp) REVERT: C 333 PHE cc_start: 0.8831 (m-10) cc_final: 0.8622 (m-10) REVERT: C 498 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7958 (ttmt) REVERT: C 544 SER cc_start: 0.8393 (p) cc_final: 0.7999 (p) REVERT: C 545 ASP cc_start: 0.7974 (t0) cc_final: 0.7682 (t0) REVERT: C 674 ASN cc_start: 0.8204 (m110) cc_final: 0.7891 (m-40) REVERT: C 711 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8023 (ttm-80) REVERT: C 781 MET cc_start: 0.8489 (ttm) cc_final: 0.8128 (ttp) REVERT: C 831 VAL cc_start: 0.8541 (p) cc_final: 0.8311 (t) REVERT: C 865 MET cc_start: 0.8631 (mtm) cc_final: 0.8377 (mtp) REVERT: C 881 MET cc_start: 0.8502 (ptp) cc_final: 0.8295 (ptp) outliers start: 27 outliers final: 14 residues processed: 295 average time/residue: 0.4526 time to fit residues: 145.4372 Evaluate side-chains 293 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 GLN C 456 GLN C 493 ASN C 877 GLN C 911 GLN C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094680 restraints weight = 16379.613| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.37 r_work: 0.3111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11000 Z= 0.200 Angle : 0.674 9.971 15011 Z= 0.326 Chirality : 0.049 0.295 1830 Planarity : 0.004 0.078 1838 Dihedral : 4.933 19.092 1378 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.59 % Allowed : 19.01 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.22), residues: 1298 helix: -2.84 (0.30), residues: 226 sheet: -2.67 (0.29), residues: 290 loop : -1.39 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 917 TYR 0.019 0.002 TYR C 533 PHE 0.022 0.002 PHE A 224 TRP 0.009 0.001 TRP A 28 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (10950) covalent geometry : angle 0.65493 / 0.32 (14866) SS BOND : bond 0.00836 / 0.46 ( 5) SS BOND : angle 2.64122 / 1.41 ( 10) hydrogen bonds : bond 0.03436 / 2.21 ( 185) hydrogen bonds : angle 5.23971 / 3.65 ( 360) link_ALPHA1-2 : bond 0.00190 / 0.12 ( 1) link_ALPHA1-2 : angle 1.85188 / 0.98 ( 3) link_ALPHA1-3 : bond 0.00561 / 0.33 ( 3) link_ALPHA1-3 : angle 1.37301 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00172 / 0.09 ( 3) link_ALPHA1-6 : angle 1.54897 / 0.97 ( 9) link_BETA1-4 : bond 0.00485 / 0.31 ( 16) link_BETA1-4 : angle 1.44823 / 0.88 ( 48) link_NAG-ASN : bond 0.00422 / 0.27 ( 22) link_NAG-ASN : angle 1.86135 / 1.26 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8975 (m-80) cc_final: 0.8672 (m-80) REVERT: A 69 TYR cc_start: 0.8917 (p90) cc_final: 0.8569 (p90) REVERT: A 122 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8224 (t0) REVERT: C 74 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8354 (mmmm) REVERT: C 83 ASP cc_start: 0.8283 (p0) cc_final: 0.7983 (p0) REVERT: C 103 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8233 (ttmm) REVERT: C 123 GLU cc_start: 0.7836 (pp20) cc_final: 0.7387 (pp20) REVERT: C 333 PHE cc_start: 0.8838 (m-10) cc_final: 0.8635 (m-10) REVERT: C 498 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7987 (ttmt) REVERT: C 544 SER cc_start: 0.8399 (p) cc_final: 0.7994 (p) REVERT: C 545 ASP cc_start: 0.7984 (t0) cc_final: 0.7668 (t0) REVERT: C 660 ASN cc_start: 0.7628 (t0) cc_final: 0.7297 (m110) REVERT: C 674 ASN cc_start: 0.8193 (m110) cc_final: 0.7910 (m-40) REVERT: C 711 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: C 781 MET cc_start: 0.8517 (ttm) cc_final: 0.8182 (ttp) REVERT: C 831 VAL cc_start: 0.8657 (p) cc_final: 0.8422 (t) REVERT: C 865 MET cc_start: 0.8660 (mtm) cc_final: 0.8383 (mtp) REVERT: C 881 MET cc_start: 0.8525 (ptp) cc_final: 0.8317 (ptp) outliers start: 30 outliers final: 18 residues processed: 289 average time/residue: 0.3940 time to fit residues: 124.6546 Evaluate side-chains 295 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN C 279 GLN C 456 GLN C 801 ASN C 877 GLN C 911 GLN C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095964 restraints weight = 16403.417| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.37 r_work: 0.3132 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11000 Z= 0.126 Angle : 0.643 9.790 15011 Z= 0.312 Chirality : 0.046 0.276 1830 Planarity : 0.004 0.079 1838 Dihedral : 4.749 18.522 1378 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.25 % Allowed : 19.71 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.22), residues: 1298 helix: -2.80 (0.30), residues: 226 sheet: -2.77 (0.29), residues: 299 loop : -1.26 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 917 TYR 0.016 0.001 TYR C 533 PHE 0.015 0.001 PHE A 224 TRP 0.008 0.001 TRP B 62 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10950) covalent geometry : angle 0.62825 / 0.31 (14866) SS BOND : bond 0.00804 / 0.44 ( 5) SS BOND : angle 2.14329 / 1.17 ( 10) hydrogen bonds : bond 0.02959 / 1.88 ( 185) hydrogen bonds : angle 5.10721 / 3.55 ( 360) link_ALPHA1-2 : bond 0.00146 / 0.09 ( 1) link_ALPHA1-2 : angle 1.81813 / 0.98 ( 3) link_ALPHA1-3 : bond 0.00549 / 0.32 ( 3) link_ALPHA1-3 : angle 1.39177 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00258 / 0.14 ( 3) link_ALPHA1-6 : angle 1.52489 / 0.97 ( 9) link_BETA1-4 : bond 0.00495 / 0.32 ( 16) link_BETA1-4 : angle 1.34376 / 0.83 ( 48) link_NAG-ASN : bond 0.00370 / 0.23 ( 22) link_NAG-ASN : angle 1.57191 / 1.06 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8979 (m-80) cc_final: 0.8699 (m-80) REVERT: A 66 HIS cc_start: 0.8636 (p90) cc_final: 0.7982 (p90) REVERT: A 69 TYR cc_start: 0.8911 (p90) cc_final: 0.8596 (p90) REVERT: A 122 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8232 (t0) REVERT: C 74 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8313 (mmmm) REVERT: C 83 ASP cc_start: 0.8261 (p0) cc_final: 0.8005 (p0) REVERT: C 103 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8210 (ttmm) REVERT: C 123 GLU cc_start: 0.7702 (pp20) cc_final: 0.7297 (pp20) REVERT: C 189 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7704 (tm) REVERT: C 249 GLU cc_start: 0.7471 (mp0) cc_final: 0.7262 (mp0) REVERT: C 333 PHE cc_start: 0.8825 (m-10) cc_final: 0.8562 (m-80) REVERT: C 498 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7970 (ttmt) REVERT: C 544 SER cc_start: 0.8401 (p) cc_final: 0.8007 (p) REVERT: C 545 ASP cc_start: 0.7994 (t0) cc_final: 0.7701 (t0) REVERT: C 674 ASN cc_start: 0.8172 (m110) cc_final: 0.7828 (t160) REVERT: C 711 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: C 768 PHE cc_start: 0.8807 (m-10) cc_final: 0.8566 (m-80) REVERT: C 781 MET cc_start: 0.8488 (ttm) cc_final: 0.8066 (ttp) REVERT: C 831 VAL cc_start: 0.8625 (p) cc_final: 0.8389 (t) REVERT: C 865 MET cc_start: 0.8650 (mtm) cc_final: 0.8399 (mtp) REVERT: C 881 MET cc_start: 0.8531 (ptp) cc_final: 0.8330 (ptp) REVERT: B 170 GLN cc_start: 0.8429 (mt0) cc_final: 0.8130 (mt0) outliers start: 26 outliers final: 17 residues processed: 294 average time/residue: 0.4243 time to fit residues: 136.0007 Evaluate side-chains 298 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 279 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 70 optimal weight: 0.0030 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 456 GLN C 612 GLN C 877 GLN C 911 GLN C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095879 restraints weight = 16369.991| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.39 r_work: 0.3126 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11000 Z= 0.135 Angle : 0.657 9.841 15011 Z= 0.318 Chirality : 0.048 0.554 1830 Planarity : 0.004 0.085 1838 Dihedral : 4.737 18.259 1378 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.42 % Allowed : 19.71 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.22), residues: 1298 helix: -2.80 (0.30), residues: 226 sheet: -2.70 (0.28), residues: 312 loop : -1.26 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 917 TYR 0.016 0.001 TYR C 533 PHE 0.017 0.001 PHE A 224 TRP 0.008 0.001 TRP B 62 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (10950) covalent geometry : angle 0.63341 / 0.31 (14866) SS BOND : bond 0.00854 / 0.46 ( 5) SS BOND : angle 3.07056 / 1.87 ( 10) hydrogen bonds : bond 0.02991 / 1.91 ( 185) hydrogen bonds : angle 5.07698 / 3.53 ( 360) link_ALPHA1-2 : bond 0.00107 / 0.07 ( 1) link_ALPHA1-2 : angle 1.79226 / 0.96 ( 3) link_ALPHA1-3 : bond 0.00541 / 0.31 ( 3) link_ALPHA1-3 : angle 1.38473 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00245 / 0.13 ( 3) link_ALPHA1-6 : angle 1.52819 / 0.97 ( 9) link_BETA1-4 : bond 0.00497 / 0.32 ( 16) link_BETA1-4 : angle 1.34672 / 0.83 ( 48) link_NAG-ASN : bond 0.00403 / 0.24 ( 22) link_NAG-ASN : angle 2.04979 / 1.46 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8981 (m-80) cc_final: 0.8692 (m-80) REVERT: A 66 HIS cc_start: 0.8648 (p90) cc_final: 0.7975 (p90) REVERT: A 69 TYR cc_start: 0.8907 (p90) cc_final: 0.8528 (p90) REVERT: A 122 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8240 (t0) REVERT: C 40 GLU cc_start: 0.8188 (tp30) cc_final: 0.7481 (tm-30) REVERT: C 74 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8305 (mmmm) REVERT: C 83 ASP cc_start: 0.8260 (p0) cc_final: 0.8009 (p0) REVERT: C 103 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8210 (ttmm) REVERT: C 123 GLU cc_start: 0.7717 (pp20) cc_final: 0.7339 (pp20) REVERT: C 189 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7804 (tm) REVERT: C 333 PHE cc_start: 0.8826 (m-10) cc_final: 0.8557 (m-80) REVERT: C 498 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7973 (ttmt) REVERT: C 544 SER cc_start: 0.8407 (p) cc_final: 0.7995 (p) REVERT: C 545 ASP cc_start: 0.8027 (t0) cc_final: 0.7730 (t0) REVERT: C 660 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7224 (m-40) REVERT: C 674 ASN cc_start: 0.8190 (m110) cc_final: 0.7820 (t0) REVERT: C 711 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: C 742 CYS cc_start: 0.7805 (m) cc_final: 0.7280 (m) REVERT: C 764 CYS cc_start: 0.6994 (p) cc_final: 0.6787 (p) REVERT: C 768 PHE cc_start: 0.8801 (m-10) cc_final: 0.8570 (m-80) REVERT: C 781 MET cc_start: 0.8500 (ttm) cc_final: 0.8063 (ttp) REVERT: C 831 VAL cc_start: 0.8649 (p) cc_final: 0.8419 (t) REVERT: C 865 MET cc_start: 0.8652 (mtm) cc_final: 0.8401 (mtp) REVERT: C 881 MET cc_start: 0.8519 (ptp) cc_final: 0.8319 (ptp) REVERT: B 170 GLN cc_start: 0.8416 (mt0) cc_final: 0.8114 (mt0) outliers start: 28 outliers final: 18 residues processed: 294 average time/residue: 0.4166 time to fit residues: 134.1694 Evaluate side-chains 302 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 280 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 612 GLN Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN C 279 GLN C 456 GLN C 786 GLN C 877 GLN C 911 GLN C 923 ASN B 36 ASN B 151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092222 restraints weight = 16580.154| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.37 r_work: 0.3071 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 11000 Z= 0.384 Angle : 0.815 10.292 15011 Z= 0.394 Chirality : 0.055 0.374 1830 Planarity : 0.005 0.092 1838 Dihedral : 5.445 19.739 1378 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 2.07 % Allowed : 20.31 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.22), residues: 1298 helix: -2.91 (0.30), residues: 219 sheet: -2.89 (0.28), residues: 301 loop : -1.44 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 917 TYR 0.023 0.002 TYR C 533 PHE 0.033 0.003 PHE A 224 TRP 0.018 0.002 TRP A 28 HIS 0.009 0.002 HIS C 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00894 / 0.38 (10950) covalent geometry : angle 0.78806 / 0.39 (14866) SS BOND : bond 0.01093 / 0.57 ( 5) SS BOND : angle 4.52297 / 2.68 ( 10) hydrogen bonds : bond 0.04352 / 2.83 ( 185) hydrogen bonds : angle 5.36905 / 3.73 ( 360) link_ALPHA1-2 : bond 0.00260 / 0.16 ( 1) link_ALPHA1-2 : angle 1.96055 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00547 / 0.32 ( 3) link_ALPHA1-3 : angle 1.38540 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00187 / 0.11 ( 3) link_ALPHA1-6 : angle 1.60330 / 1.00 ( 9) link_BETA1-4 : bond 0.00543 / 0.33 ( 16) link_BETA1-4 : angle 1.69322 / 0.99 ( 48) link_NAG-ASN : bond 0.00633 / 0.43 ( 22) link_NAG-ASN : angle 2.31087 / 1.61 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8995 (m-80) cc_final: 0.8636 (m-80) REVERT: A 69 TYR cc_start: 0.8942 (p90) cc_final: 0.8647 (p90) REVERT: C 74 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (mmmm) REVERT: C 83 ASP cc_start: 0.8297 (p0) cc_final: 0.8020 (p0) REVERT: C 103 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8267 (ttmm) REVERT: C 123 GLU cc_start: 0.7792 (pp20) cc_final: 0.7402 (pp20) REVERT: C 353 MET cc_start: 0.8492 (mtm) cc_final: 0.8157 (mtm) REVERT: C 498 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8040 (ttmt) REVERT: C 544 SER cc_start: 0.8401 (p) cc_final: 0.7992 (p) REVERT: C 545 ASP cc_start: 0.8054 (t0) cc_final: 0.7758 (t0) REVERT: C 674 ASN cc_start: 0.8292 (m110) cc_final: 0.8008 (m-40) REVERT: C 711 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7980 (ttm-80) REVERT: C 781 MET cc_start: 0.8594 (ttm) cc_final: 0.8266 (ttp) REVERT: C 831 VAL cc_start: 0.8754 (p) cc_final: 0.8543 (t) REVERT: C 865 MET cc_start: 0.8755 (mtm) cc_final: 0.8466 (mtp) REVERT: C 881 MET cc_start: 0.8532 (ptp) cc_final: 0.8329 (ptp) outliers start: 24 outliers final: 17 residues processed: 290 average time/residue: 0.4259 time to fit residues: 135.5934 Evaluate side-chains 286 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.0050 chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 43 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 GLN C 456 GLN C 612 GLN C 786 GLN C 801 ASN C 911 GLN C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095768 restraints weight = 16518.211| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.40 r_work: 0.3133 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11000 Z= 0.116 Angle : 0.672 9.787 15011 Z= 0.325 Chirality : 0.047 0.358 1830 Planarity : 0.004 0.082 1838 Dihedral : 4.826 18.958 1378 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.73 % Allowed : 21.43 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.22), residues: 1298 helix: -2.78 (0.30), residues: 224 sheet: -2.68 (0.29), residues: 299 loop : -1.37 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 917 TYR 0.023 0.002 TYR A 34 PHE 0.012 0.001 PHE A 224 TRP 0.012 0.001 TRP C 328 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (10950) covalent geometry : angle 0.65314 / 0.32 (14866) SS BOND : bond 0.00764 / 0.41 ( 5) SS BOND : angle 2.38800 / 1.42 ( 10) hydrogen bonds : bond 0.02915 / 1.85 ( 185) hydrogen bonds : angle 5.18178 / 3.62 ( 360) link_ALPHA1-2 : bond 0.00207 / 0.13 ( 1) link_ALPHA1-2 : angle 1.72685 / 0.94 ( 3) link_ALPHA1-3 : bond 0.00531 / 0.31 ( 3) link_ALPHA1-3 : angle 1.40799 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00290 / 0.16 ( 3) link_ALPHA1-6 : angle 1.48226 / 0.94 ( 9) link_BETA1-4 : bond 0.00489 / 0.32 ( 16) link_BETA1-4 : angle 1.30195 / 0.81 ( 48) link_NAG-ASN : bond 0.00482 / 0.32 ( 22) link_NAG-ASN : angle 1.95697 / 1.43 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.61 seconds wall clock time: 64 minutes 21.64 seconds (3861.64 seconds total)