Starting phenix.real_space_refine on Wed Mar 4 04:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7drc_30826/03_2026/7drc_30826.cif Found real_map, /net/cci-nas-00/data/ceres_data/7drc_30826/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7drc_30826/03_2026/7drc_30826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7drc_30826/03_2026/7drc_30826.map" model { file = "/net/cci-nas-00/data/ceres_data/7drc_30826/03_2026/7drc_30826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7drc_30826/03_2026/7drc_30826.cif" } 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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 24 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 27 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.49, per 1000 atoms: 0.23 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: 0.91 Conformation dependent library (CDL) restraints added in 560.9 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: 0.46 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: 2.21 Time building geometry restraints manager: 1.26 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 - 22.94: 6611 22.94 - 45.87: 397 45.87 - 68.81: 33 68.81 - 91.75: 46 91.75 - 114.68: 45 Dihedral angle restraints: 7132 sinusoidal: 3367 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 7129 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 18.084 114.683 4693 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 covalent geometry : bond 0.00464 (10950) covalent geometry : angle 0.73642 (14866) SS BOND : bond 0.00460 ( 5) SS BOND : angle 2.38221 ( 10) hydrogen bonds : bond 0.21058 ( 185) hydrogen bonds : angle 6.98588 ( 360) link_ALPHA1-2 : bond 0.00221 ( 1) link_ALPHA1-2 : angle 2.60071 ( 3) link_ALPHA1-3 : bond 0.00404 ( 3) link_ALPHA1-3 : angle 1.61240 ( 9) link_ALPHA1-6 : bond 0.00210 ( 3) link_ALPHA1-6 : angle 2.11860 ( 9) link_BETA1-4 : bond 0.00507 ( 16) link_BETA1-4 : angle 1.52758 ( 48) link_NAG-ASN : bond 0.00384 ( 22) link_NAG-ASN : angle 2.45317 ( 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 : 0.422 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: 0.4961 time to fit residues: 162.0213 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 : 0.259 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3465 r_free = 0.3465 target = 0.109834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094534 restraints weight = 16456.095| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.41 r_work: 0.3106 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11000 Z= 0.207 Angle : 0.719 12.819 15011 Z= 0.338 Chirality : 0.051 0.241 1830 Planarity : 0.005 0.055 1838 Dihedral : 14.290 106.493 2295 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.30 % Allowed : 12.71 % Favored : 86.00 % 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: -2.69 (0.32), residues: 205 sheet: -2.75 (0.29), residues: 287 loop : -1.37 (0.21), residues: 806 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 covalent geometry : bond 0.00482 (10950) covalent geometry : angle 0.69314 (14866) SS BOND : bond 0.00598 ( 5) SS BOND : angle 2.12855 ( 10) hydrogen bonds : bond 0.04290 ( 185) hydrogen bonds : angle 5.54399 ( 360) link_ALPHA1-2 : bond 0.00309 ( 1) link_ALPHA1-2 : angle 2.40085 ( 3) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 1.99268 ( 9) link_ALPHA1-6 : bond 0.00268 ( 3) link_ALPHA1-6 : angle 1.85877 ( 9) link_BETA1-4 : bond 0.00497 ( 16) link_BETA1-4 : angle 2.21188 ( 48) link_NAG-ASN : bond 0.00558 ( 22) link_NAG-ASN : angle 1.95815 ( 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 302 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 287 time to evaluate : 0.389 Fit side-chains REVERT: A 37 TYR cc_start: 0.8951 (m-80) cc_final: 0.8644 (m-80) REVERT: A 66 HIS cc_start: 0.8652 (p90) cc_final: 0.7869 (p90) REVERT: C 103 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8127 (ttmm) REVERT: C 123 GLU cc_start: 0.7852 (pp20) cc_final: 0.7425 (pp20) REVERT: C 189 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7748 (tp) REVERT: C 498 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8050 (ttmt) REVERT: C 610 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8197 (ttpt) REVERT: C 702 ASP cc_start: 0.7980 (t0) cc_final: 0.7775 (t0) REVERT: C 711 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7994 (ttm-80) REVERT: C 764 CYS cc_start: 0.7091 (p) cc_final: 0.6789 (p) REVERT: C 781 MET cc_start: 0.8489 (ttm) cc_final: 0.8046 (ttp) REVERT: C 813 TYR cc_start: 0.8009 (t80) cc_final: 0.7761 (t80) REVERT: C 881 MET cc_start: 0.8511 (ptp) cc_final: 0.8252 (ptp) REVERT: C 932 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8060 (mm-40) REVERT: B 139 LEU cc_start: 0.8642 (tt) cc_final: 0.8390 (tp) outliers start: 15 outliers final: 7 residues processed: 292 average time/residue: 0.5050 time to fit residues: 159.8711 Evaluate side-chains 286 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 278 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN B 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095478 restraints weight = 16366.495| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.39 r_work: 0.3125 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1219 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= 0.139 Angle : 0.677 10.443 15011 Z= 0.314 Chirality : 0.049 0.257 1830 Planarity : 0.004 0.053 1838 Dihedral : 11.551 100.456 2295 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.73 % Allowed : 14.78 % Favored : 83.49 % 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: -2.64 (0.32), residues: 211 sheet: -2.86 (0.28), residues: 297 loop : -1.29 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 917 TYR 0.017 0.001 TYR C 533 PHE 0.017 0.001 PHE A 224 TRP 0.007 0.001 TRP A 65 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00318 (10950) covalent geometry : angle 0.64822 (14866) SS BOND : bond 0.00516 ( 5) SS BOND : angle 1.67864 ( 10) hydrogen bonds : bond 0.03445 ( 185) hydrogen bonds : angle 5.28100 ( 360) link_ALPHA1-2 : bond 0.00256 ( 1) link_ALPHA1-2 : angle 2.12249 ( 3) link_ALPHA1-3 : bond 0.01076 ( 3) link_ALPHA1-3 : angle 1.74747 ( 9) link_ALPHA1-6 : bond 0.00432 ( 3) link_ALPHA1-6 : angle 1.89251 ( 9) link_BETA1-4 : bond 0.00506 ( 16) link_BETA1-4 : angle 2.08937 ( 48) link_NAG-ASN : bond 0.00542 ( 22) link_NAG-ASN : angle 2.21862 ( 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 297 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8961 (m-80) cc_final: 0.8706 (m-80) REVERT: A 66 HIS cc_start: 0.8626 (p90) cc_final: 0.7932 (p90) REVERT: C 74 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8398 (mmmm) REVERT: C 103 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8170 (ttmm) REVERT: C 123 GLU cc_start: 0.7925 (pp20) cc_final: 0.7464 (pp20) REVERT: C 189 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7739 (tp) REVERT: C 280 ILE cc_start: 0.8715 (mt) cc_final: 0.8514 (mm) REVERT: C 498 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8007 (ttmt) REVERT: C 544 SER cc_start: 0.8381 (p) cc_final: 0.7975 (p) REVERT: C 660 ASN cc_start: 0.7340 (p0) cc_final: 0.7088 (t0) REVERT: C 702 ASP cc_start: 0.7994 (t0) cc_final: 0.7732 (t0) REVERT: C 711 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: C 781 MET cc_start: 0.8462 (ttm) cc_final: 0.8145 (ttp) REVERT: C 881 MET cc_start: 0.8498 (ptp) cc_final: 0.8266 (ptp) REVERT: B 139 LEU cc_start: 0.8672 (tt) cc_final: 0.8392 (tp) outliers start: 20 outliers final: 8 residues processed: 281 average time/residue: 0.4794 time to fit residues: 146.2670 Evaluate side-chains 291 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 282 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 931 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 88 optimal weight: 0.0010 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 279 GLN C 297 ASN C 456 GLN C 877 GLN C 911 GLN B 86 GLN B 151 ASN B 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096688 restraints weight = 16390.390| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.41 r_work: 0.3139 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11000 Z= 0.107 Angle : 0.617 9.956 15011 Z= 0.290 Chirality : 0.048 0.301 1830 Planarity : 0.004 0.052 1838 Dihedral : 9.335 91.354 2295 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.85 % Allowed : 15.38 % Favored : 81.76 % 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: -2.80 (0.23), residues: 1298 helix: -2.55 (0.33), residues: 205 sheet: -2.80 (0.29), residues: 302 loop : -1.21 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 917 TYR 0.014 0.001 TYR C 533 PHE 0.012 0.001 PHE A 224 TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00239 (10950) covalent geometry : angle 0.59441 (14866) SS BOND : bond 0.00416 ( 5) SS BOND : angle 1.32393 ( 10) hydrogen bonds : bond 0.02815 ( 185) hydrogen bonds : angle 5.01102 ( 360) link_ALPHA1-2 : bond 0.00223 ( 1) link_ALPHA1-2 : angle 2.01700 ( 3) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 1.89266 ( 9) link_ALPHA1-6 : bond 0.00589 ( 3) link_ALPHA1-6 : angle 1.92275 ( 9) link_BETA1-4 : bond 0.00473 ( 16) link_BETA1-4 : angle 1.97907 ( 48) link_NAG-ASN : bond 0.00583 ( 22) link_NAG-ASN : angle 1.68700 ( 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 328 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8944 (m-80) cc_final: 0.8711 (m-80) REVERT: A 66 HIS cc_start: 0.8584 (p90) cc_final: 0.7962 (p90) REVERT: A 69 TYR cc_start: 0.8937 (p90) cc_final: 0.8504 (p90) REVERT: C 40 GLU cc_start: 0.8175 (tp30) cc_final: 0.7450 (tm-30) REVERT: C 74 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8355 (mmmm) REVERT: C 83 ASP cc_start: 0.8311 (p0) cc_final: 0.8065 (p0) REVERT: C 103 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8182 (ttmm) REVERT: C 123 GLU cc_start: 0.7951 (pp20) cc_final: 0.7530 (pp20) REVERT: C 187 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8077 (mt) REVERT: C 464 ASP cc_start: 0.7804 (t0) cc_final: 0.7569 (t70) REVERT: C 498 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7949 (ttmt) REVERT: C 544 SER cc_start: 0.8395 (p) cc_final: 0.8004 (p) REVERT: C 660 ASN cc_start: 0.7233 (p0) cc_final: 0.6809 (t0) REVERT: C 662 SER cc_start: 0.8305 (t) cc_final: 0.8088 (m) REVERT: C 674 ASN cc_start: 0.8172 (m110) cc_final: 0.7744 (t160) REVERT: C 702 ASP cc_start: 0.7966 (t0) cc_final: 0.7659 (t0) REVERT: C 711 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8026 (ttm-80) REVERT: C 781 MET cc_start: 0.8460 (ttm) cc_final: 0.8142 (ttp) REVERT: C 831 VAL cc_start: 0.8428 (t) cc_final: 0.8208 (p) REVERT: C 841 MET cc_start: 0.8579 (mtp) cc_final: 0.8349 (mtm) REVERT: C 881 MET cc_start: 0.8526 (ptp) cc_final: 0.8314 (ptp) REVERT: B 139 LEU cc_start: 0.8704 (tt) cc_final: 0.8448 (tp) outliers start: 33 outliers final: 14 residues processed: 308 average time/residue: 0.4671 time to fit residues: 157.1063 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 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain B residue 57 VAL 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: 4.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS 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** B 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092787 restraints weight = 16434.018| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.38 r_work: 0.3078 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11000 Z= 0.350 Angle : 0.782 10.345 15011 Z= 0.372 Chirality : 0.055 0.313 1830 Planarity : 0.005 0.067 1838 Dihedral : 9.401 84.796 2295 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.28 % Allowed : 17.03 % Favored : 79.69 % 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: -2.98 (0.22), residues: 1298 helix: -2.75 (0.31), residues: 211 sheet: -2.82 (0.28), residues: 294 loop : -1.37 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 917 TYR 0.022 0.002 TYR C 533 PHE 0.031 0.002 PHE A 224 TRP 0.015 0.002 TRP A 28 HIS 0.009 0.002 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00814 (10950) covalent geometry : angle 0.75212 (14866) SS BOND : bond 0.00854 ( 5) SS BOND : angle 3.29225 ( 10) hydrogen bonds : bond 0.04202 ( 185) hydrogen bonds : angle 5.42926 ( 360) link_ALPHA1-2 : bond 0.00274 ( 1) link_ALPHA1-2 : angle 2.14180 ( 3) link_ALPHA1-3 : bond 0.01039 ( 3) link_ALPHA1-3 : angle 1.86493 ( 9) link_ALPHA1-6 : bond 0.00385 ( 3) link_ALPHA1-6 : angle 1.85870 ( 9) link_BETA1-4 : bond 0.00471 ( 16) link_BETA1-4 : angle 2.19117 ( 48) link_NAG-ASN : bond 0.00545 ( 22) link_NAG-ASN : angle 2.29599 ( 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 328 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8996 (m-80) cc_final: 0.8715 (m-80) REVERT: C 65 CYS cc_start: 0.8318 (m) cc_final: 0.7720 (t) REVERT: C 74 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8402 (mmmm) REVERT: C 83 ASP cc_start: 0.8325 (p0) cc_final: 0.8022 (p0) REVERT: C 103 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8273 (ttmm) REVERT: C 123 GLU cc_start: 0.7866 (pp20) cc_final: 0.7351 (pp20) REVERT: C 498 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8015 (ttmt) REVERT: C 545 ASP cc_start: 0.7978 (t0) cc_final: 0.7708 (t0) REVERT: C 660 ASN cc_start: 0.7375 (p0) cc_final: 0.7149 (t0) REVERT: C 674 ASN cc_start: 0.8227 (m110) cc_final: 0.7939 (m-40) REVERT: C 702 ASP cc_start: 0.8007 (t0) cc_final: 0.7716 (t0) REVERT: C 711 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8017 (ttm-80) REVERT: C 781 MET cc_start: 0.8580 (ttm) cc_final: 0.8220 (ttp) REVERT: C 881 MET cc_start: 0.8537 (ptp) cc_final: 0.8337 (ptp) outliers start: 38 outliers final: 20 residues processed: 304 average time/residue: 0.4632 time to fit residues: 154.0693 Evaluate side-chains 291 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 653 VAL 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 119 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 142 LEU 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: 0.7980 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 279 GLN C 456 GLN C 911 GLN C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095180 restraints weight = 16395.594| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.40 r_work: 0.3119 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11000 Z= 0.134 Angle : 0.667 9.948 15011 Z= 0.319 Chirality : 0.049 0.392 1830 Planarity : 0.004 0.064 1838 Dihedral : 8.783 82.395 2295 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.59 % Allowed : 18.93 % Favored : 78.48 % 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: 210 sheet: -2.74 (0.29), residues: 292 loop : -1.34 (0.21), residues: 796 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 covalent geometry : bond 0.00313 (10950) covalent geometry : angle 0.64353 (14866) SS BOND : bond 0.00782 ( 5) SS BOND : angle 2.82894 ( 10) hydrogen bonds : bond 0.03185 ( 185) hydrogen bonds : angle 5.28573 ( 360) link_ALPHA1-2 : bond 0.00334 ( 1) link_ALPHA1-2 : angle 2.08155 ( 3) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 1.95467 ( 9) link_ALPHA1-6 : bond 0.00635 ( 3) link_ALPHA1-6 : angle 1.88432 ( 9) link_BETA1-4 : bond 0.00490 ( 16) link_BETA1-4 : angle 1.85152 ( 48) link_NAG-ASN : bond 0.00464 ( 22) link_NAG-ASN : angle 1.71962 ( 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 314 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8964 (m-80) cc_final: 0.8688 (m-80) REVERT: A 122 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8241 (t0) REVERT: C 74 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8354 (mmmm) REVERT: C 83 ASP cc_start: 0.8280 (p0) cc_final: 0.8012 (p0) REVERT: C 103 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8335 (tttm) REVERT: C 123 GLU cc_start: 0.7725 (pp20) cc_final: 0.7316 (pp20) REVERT: C 498 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7979 (ttmt) REVERT: C 544 SER cc_start: 0.8399 (p) cc_final: 0.8009 (p) REVERT: C 545 ASP cc_start: 0.7982 (t0) cc_final: 0.7698 (t0) REVERT: C 660 ASN cc_start: 0.7257 (p0) cc_final: 0.6942 (t0) REVERT: C 674 ASN cc_start: 0.8183 (m110) cc_final: 0.7891 (m-40) REVERT: C 702 ASP cc_start: 0.7967 (t0) cc_final: 0.7660 (t0) REVERT: C 711 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: C 781 MET cc_start: 0.8509 (ttm) cc_final: 0.8103 (ttp) REVERT: C 845 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8161 (mtpp) REVERT: C 855 ASN cc_start: 0.7772 (p0) cc_final: 0.7450 (p0) REVERT: C 881 MET cc_start: 0.8546 (ptp) cc_final: 0.8339 (ptp) REVERT: B 170 GLN cc_start: 0.8463 (mt0) cc_final: 0.8170 (mt0) outliers start: 30 outliers final: 15 residues processed: 296 average time/residue: 0.4718 time to fit residues: 152.1925 Evaluate side-chains 297 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 281 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 232 ILE 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 931 LEU Chi-restraints excluded: chain B residue 119 THR 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: 0.5980 chunk 65 optimal weight: 2.9990 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: 1.9990 chunk 98 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 297 ASN 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 = 0.3458 r_free = 0.3458 target = 0.109705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094338 restraints weight = 16379.803| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.38 r_work: 0.3104 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1663 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= 0.201 Angle : 0.692 10.178 15011 Z= 0.333 Chirality : 0.050 0.304 1830 Planarity : 0.004 0.076 1838 Dihedral : 8.569 79.874 2295 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.59 % Allowed : 19.71 % Favored : 77.70 % 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: -2.98 (0.22), residues: 1298 helix: -2.79 (0.30), residues: 220 sheet: -2.78 (0.28), residues: 309 loop : -1.30 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 917 TYR 0.018 0.002 TYR C 533 PHE 0.023 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 covalent geometry : bond 0.00474 (10950) covalent geometry : angle 0.66941 (14866) SS BOND : bond 0.00883 ( 5) SS BOND : angle 2.71376 ( 10) hydrogen bonds : bond 0.03478 ( 185) hydrogen bonds : angle 5.26526 ( 360) link_ALPHA1-2 : bond 0.00295 ( 1) link_ALPHA1-2 : angle 2.12856 ( 3) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 1.92521 ( 9) link_ALPHA1-6 : bond 0.00560 ( 3) link_ALPHA1-6 : angle 1.86477 ( 9) link_BETA1-4 : bond 0.00436 ( 16) link_BETA1-4 : angle 1.86408 ( 48) link_NAG-ASN : bond 0.00525 ( 22) link_NAG-ASN : angle 1.75231 ( 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 318 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8980 (m-80) cc_final: 0.8734 (m-80) REVERT: A 108 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 122 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8220 (t0) REVERT: C 74 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8374 (mmmm) REVERT: C 83 ASP cc_start: 0.8265 (p0) cc_final: 0.7999 (p0) REVERT: C 123 GLU cc_start: 0.7750 (pp20) cc_final: 0.7295 (pp20) REVERT: C 249 GLU cc_start: 0.7522 (mp0) cc_final: 0.7315 (mp0) REVERT: C 498 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7994 (ttmt) REVERT: C 544 SER cc_start: 0.8393 (p) cc_final: 0.7989 (p) REVERT: C 545 ASP cc_start: 0.7992 (t0) cc_final: 0.7679 (t0) REVERT: C 674 ASN cc_start: 0.8191 (m110) cc_final: 0.7916 (m-40) REVERT: C 702 ASP cc_start: 0.7996 (t0) cc_final: 0.7686 (t0) REVERT: C 711 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8026 (ttm-80) REVERT: C 781 MET cc_start: 0.8535 (ttm) cc_final: 0.8184 (ttp) REVERT: C 831 VAL cc_start: 0.8562 (p) cc_final: 0.8345 (t) REVERT: C 855 ASN cc_start: 0.7645 (p0) cc_final: 0.7372 (p0) REVERT: C 881 MET cc_start: 0.8523 (ptp) cc_final: 0.8313 (ptp) REVERT: B 170 GLN cc_start: 0.8456 (mt0) cc_final: 0.8166 (mt0) outliers start: 30 outliers final: 21 residues processed: 300 average time/residue: 0.4708 time to fit residues: 154.1621 Evaluate side-chains 307 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain A residue 108 TYR 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 232 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.0010 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094344 restraints weight = 16450.442| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.39 r_work: 0.3104 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11000 Z= 0.201 Angle : 0.738 16.571 15011 Z= 0.347 Chirality : 0.051 0.289 1830 Planarity : 0.004 0.080 1838 Dihedral : 8.451 77.991 2295 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.51 % Allowed : 20.57 % Favored : 76.92 % 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: -3.02 (0.22), residues: 1298 helix: -2.78 (0.30), residues: 218 sheet: -2.75 (0.30), residues: 278 loop : -1.46 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 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 covalent geometry : bond 0.00472 (10950) covalent geometry : angle 0.68932 (14866) SS BOND : bond 0.00877 ( 5) SS BOND : angle 2.65123 ( 10) hydrogen bonds : bond 0.03464 ( 185) hydrogen bonds : angle 5.26037 ( 360) link_ALPHA1-2 : bond 0.00318 ( 1) link_ALPHA1-2 : angle 2.10358 ( 3) link_ALPHA1-3 : bond 0.01033 ( 3) link_ALPHA1-3 : angle 1.93254 ( 9) link_ALPHA1-6 : bond 0.00578 ( 3) link_ALPHA1-6 : angle 1.85741 ( 9) link_BETA1-4 : bond 0.00425 ( 16) link_BETA1-4 : angle 1.83147 ( 48) link_NAG-ASN : bond 0.00413 ( 22) link_NAG-ASN : angle 3.50605 ( 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 316 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8983 (m-80) cc_final: 0.8746 (m-80) REVERT: A 69 TYR cc_start: 0.8875 (p90) cc_final: 0.8328 (p90) REVERT: A 108 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 122 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8244 (t0) REVERT: C 74 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8320 (mmmm) REVERT: C 83 ASP cc_start: 0.8248 (p0) cc_final: 0.7988 (p0) REVERT: C 123 GLU cc_start: 0.7762 (pp20) cc_final: 0.7313 (pp20) REVERT: C 498 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7994 (ttmt) REVERT: C 544 SER cc_start: 0.8407 (p) cc_final: 0.8017 (p) REVERT: C 545 ASP cc_start: 0.8012 (t0) cc_final: 0.7717 (t0) REVERT: C 660 ASN cc_start: 0.7647 (t0) cc_final: 0.7263 (t0) REVERT: C 674 ASN cc_start: 0.8207 (m110) cc_final: 0.7913 (m-40) REVERT: C 702 ASP cc_start: 0.7994 (t0) cc_final: 0.7683 (t0) REVERT: C 711 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8017 (ttm-80) REVERT: C 768 PHE cc_start: 0.8806 (m-10) cc_final: 0.8545 (m-80) REVERT: C 781 MET cc_start: 0.8534 (ttm) cc_final: 0.8170 (ttp) REVERT: C 831 VAL cc_start: 0.8630 (p) cc_final: 0.8406 (t) REVERT: C 855 ASN cc_start: 0.7624 (p0) cc_final: 0.7341 (p0) REVERT: C 881 MET cc_start: 0.8531 (ptp) cc_final: 0.8329 (ptp) REVERT: B 170 GLN cc_start: 0.8458 (mt0) cc_final: 0.8171 (mt0) outliers start: 29 outliers final: 21 residues processed: 299 average time/residue: 0.4688 time to fit residues: 153.2485 Evaluate side-chains 301 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR 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 232 ILE 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 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 119 THR 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: 0.6980 chunk 118 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 0.0060 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 456 GLN C 801 ASN C 877 GLN C 911 GLN C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 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 = 0.111647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096233 restraints weight = 16404.039| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.41 r_work: 0.3132 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11000 Z= 0.115 Angle : 0.672 12.799 15011 Z= 0.319 Chirality : 0.048 0.257 1830 Planarity : 0.004 0.079 1838 Dihedral : 7.972 74.649 2295 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.99 % Allowed : 21.35 % Favored : 76.66 % 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 (0.23), residues: 1298 helix: -2.71 (0.31), residues: 218 sheet: -2.70 (0.29), residues: 298 loop : -1.32 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 917 TYR 0.014 0.001 TYR C 533 PHE 0.012 0.001 PHE A 224 TRP 0.009 0.001 TRP C 328 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00268 (10950) covalent geometry : angle 0.63872 (14866) SS BOND : bond 0.00739 ( 5) SS BOND : angle 1.86688 ( 10) hydrogen bonds : bond 0.02831 ( 185) hydrogen bonds : angle 5.13603 ( 360) link_ALPHA1-2 : bond 0.00211 ( 1) link_ALPHA1-2 : angle 2.03787 ( 3) link_ALPHA1-3 : bond 0.01024 ( 3) link_ALPHA1-3 : angle 1.91937 ( 9) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 1.90992 ( 9) link_BETA1-4 : bond 0.00464 ( 16) link_BETA1-4 : angle 1.70104 ( 48) link_NAG-ASN : bond 0.00406 ( 22) link_NAG-ASN : angle 2.61637 ( 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 321 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8970 (m-80) cc_final: 0.8688 (m-80) REVERT: A 66 HIS cc_start: 0.8657 (p-80) cc_final: 0.8028 (p90) REVERT: A 108 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 122 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8232 (t0) REVERT: A 228 ASN cc_start: 0.8558 (t0) cc_final: 0.8232 (t0) REVERT: C 40 GLU cc_start: 0.8177 (tp30) cc_final: 0.7473 (tm-30) REVERT: C 74 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8325 (mmmm) REVERT: C 83 ASP cc_start: 0.8252 (p0) cc_final: 0.8024 (p0) REVERT: C 123 GLU cc_start: 0.7677 (pp20) cc_final: 0.7319 (pp20) REVERT: C 333 PHE cc_start: 0.8825 (m-10) cc_final: 0.8585 (m-10) REVERT: C 498 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7993 (ttmt) REVERT: C 544 SER cc_start: 0.8403 (p) cc_final: 0.8006 (p) REVERT: C 545 ASP cc_start: 0.8017 (t0) cc_final: 0.7722 (t0) REVERT: C 660 ASN cc_start: 0.7728 (t0) cc_final: 0.7386 (t0) REVERT: C 674 ASN cc_start: 0.8183 (m110) cc_final: 0.7811 (t0) REVERT: C 702 ASP cc_start: 0.7974 (t0) cc_final: 0.7658 (t0) REVERT: C 711 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8044 (ttm-80) REVERT: C 768 PHE cc_start: 0.8786 (m-10) cc_final: 0.8551 (m-80) REVERT: C 781 MET cc_start: 0.8473 (ttm) cc_final: 0.8005 (ttp) REVERT: C 831 VAL cc_start: 0.8497 (p) cc_final: 0.8288 (t) REVERT: C 855 ASN cc_start: 0.7680 (p0) cc_final: 0.7390 (p0) REVERT: C 865 MET cc_start: 0.8671 (mtp) cc_final: 0.8309 (mtp) REVERT: C 881 MET cc_start: 0.8539 (ptp) cc_final: 0.8321 (ptp) REVERT: B 170 GLN cc_start: 0.8393 (mt0) cc_final: 0.8120 (mt0) outliers start: 23 outliers final: 15 residues processed: 306 average time/residue: 0.4591 time to fit residues: 153.8630 Evaluate side-chains 312 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 108 TYR 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 80 ILE 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 525 LYS Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 119 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: 1.9990 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 456 GLN C 877 GLN C 911 GLN C 923 ASN B 86 GLN B 129 ASN B 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095719 restraints weight = 16335.513| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.36 r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11000 Z= 0.149 Angle : 0.688 11.201 15011 Z= 0.327 Chirality : 0.048 0.273 1830 Planarity : 0.004 0.086 1838 Dihedral : 7.848 71.712 2295 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.99 % Allowed : 21.43 % Favored : 76.58 % 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 (0.23), residues: 1298 helix: -2.71 (0.31), residues: 218 sheet: -2.68 (0.29), residues: 298 loop : -1.32 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 917 TYR 0.017 0.001 TYR C 533 PHE 0.018 0.001 PHE A 224 TRP 0.007 0.001 TRP A 65 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00352 (10950) covalent geometry : angle 0.65769 (14866) SS BOND : bond 0.00743 ( 5) SS BOND : angle 2.14321 ( 10) hydrogen bonds : bond 0.03057 ( 185) hydrogen bonds : angle 5.12996 ( 360) link_ALPHA1-2 : bond 0.00189 ( 1) link_ALPHA1-2 : angle 2.04271 ( 3) link_ALPHA1-3 : bond 0.00999 ( 3) link_ALPHA1-3 : angle 1.91008 ( 9) link_ALPHA1-6 : bond 0.00681 ( 3) link_ALPHA1-6 : angle 1.84903 ( 9) link_BETA1-4 : bond 0.00436 ( 16) link_BETA1-4 : angle 1.76199 ( 48) link_NAG-ASN : bond 0.00397 ( 22) link_NAG-ASN : angle 2.44772 ( 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 314 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8960 (m-80) cc_final: 0.8666 (m-80) REVERT: A 66 HIS cc_start: 0.8653 (p-80) cc_final: 0.8030 (p90) REVERT: A 108 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8462 (t80) REVERT: A 122 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8245 (t0) REVERT: A 228 ASN cc_start: 0.8595 (t0) cc_final: 0.8260 (t0) REVERT: C 40 GLU cc_start: 0.8176 (tp30) cc_final: 0.7459 (tm-30) REVERT: C 74 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8322 (mmmm) REVERT: C 83 ASP cc_start: 0.8253 (p0) cc_final: 0.8025 (p0) REVERT: C 103 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8156 (ttmm) REVERT: C 249 GLU cc_start: 0.7421 (mp0) cc_final: 0.7208 (mp0) REVERT: C 333 PHE cc_start: 0.8832 (m-10) cc_final: 0.8572 (m-80) REVERT: C 498 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7973 (ttmt) REVERT: C 544 SER cc_start: 0.8414 (p) cc_final: 0.8006 (p) REVERT: C 545 ASP cc_start: 0.8032 (t0) cc_final: 0.7745 (t0) REVERT: C 660 ASN cc_start: 0.7785 (t0) cc_final: 0.7438 (t0) REVERT: C 674 ASN cc_start: 0.8184 (m110) cc_final: 0.7902 (m-40) REVERT: C 702 ASP cc_start: 0.7980 (t0) cc_final: 0.7675 (t0) REVERT: C 711 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8007 (ttm-80) REVERT: C 768 PHE cc_start: 0.8799 (m-10) cc_final: 0.8547 (m-80) REVERT: C 781 MET cc_start: 0.8521 (ttm) cc_final: 0.8145 (ttp) REVERT: C 831 VAL cc_start: 0.8650 (p) cc_final: 0.8418 (t) REVERT: C 855 ASN cc_start: 0.7639 (p0) cc_final: 0.7357 (p0) REVERT: B 170 GLN cc_start: 0.8385 (mt0) cc_final: 0.8064 (mt0) outliers start: 23 outliers final: 17 residues processed: 298 average time/residue: 0.4894 time to fit residues: 158.8774 Evaluate side-chains 301 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 108 TYR 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 80 ILE 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 769 THR Chi-restraints excluded: chain C residue 884 LYS 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 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 456 GLN C 612 GLN C 877 GLN C 911 GLN B 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096543 restraints weight = 16465.937| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.41 r_work: 0.3137 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1900 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= 0.118 Angle : 0.659 9.851 15011 Z= 0.314 Chirality : 0.047 0.256 1830 Planarity : 0.004 0.082 1838 Dihedral : 7.507 67.119 2295 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.90 % Allowed : 21.35 % Favored : 76.75 % 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 (0.23), residues: 1298 helix: -2.69 (0.31), residues: 218 sheet: -2.67 (0.29), residues: 299 loop : -1.30 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 917 TYR 0.014 0.001 TYR C 533 PHE 0.013 0.001 PHE A 224 TRP 0.009 0.001 TRP B 62 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00277 (10950) covalent geometry : angle 0.63303 (14866) SS BOND : bond 0.00720 ( 5) SS BOND : angle 1.74364 ( 10) hydrogen bonds : bond 0.02774 ( 185) hydrogen bonds : angle 5.05413 ( 360) link_ALPHA1-2 : bond 0.00268 ( 1) link_ALPHA1-2 : angle 1.93948 ( 3) link_ALPHA1-3 : bond 0.00981 ( 3) link_ALPHA1-3 : angle 1.89808 ( 9) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 1.85314 ( 9) link_BETA1-4 : bond 0.00446 ( 16) link_BETA1-4 : angle 1.71571 ( 48) link_NAG-ASN : bond 0.00387 ( 22) link_NAG-ASN : angle 2.19743 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.71 seconds wall clock time: 69 minutes 11.41 seconds (4151.41 seconds total)