Starting phenix.real_space_refine on Thu Aug 6 14:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.cif Found real_map, /net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.map" model { file = "/net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/35te_77179/08_2026/35te_77179.cif" } resolution = 4.43 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= 0.002 sd= 0.004 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 99 5.16 5 C 9615 2.51 5 N 2611 2.21 5 O 2957 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15282 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3783 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3783 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3784 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1218 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Chain: "E" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1218 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Chain: "F" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1218 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Chain: "G" 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: "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: 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: "J" 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: "K" 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: "L" 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 Time building chain proxies: 3.58, per 1000 atoms: 0.23 Number of scatterers: 15282 At special positions: 0 Unit cell: (147.291, 174.977, 161.688, 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 99 16.00 O 2957 8.00 N 2611 7.00 C 9615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.04 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 81 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 69 " distance=2.04 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 81 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " 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 G 1 " - " ASN A 154 " " NAG H 1 " - " ASN B 154 " " NAG I 1 " - " ASN C 154 " " NAG J 1 " - " ASN D 15 " " NAG K 1 " - " ASN E 15 " " NAG L 1 " - " ASN F 15 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 498.7 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 38 sheets defined 30.1% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 4.063A pdb=" N SER A 86 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.885A pdb=" N GLY A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.849A pdb=" N THR A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.852A pdb=" N THR A 391 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 392' Processing helix chain 'A' and resid 402 through 422 removed outlier: 3.824A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 430 through 455 removed outlier: 6.119A pdb=" N GLY A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 475 Processing helix chain 'A' and resid 478 through 499 removed outlier: 3.846A pdb=" N VAL A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.995A pdb=" N SER B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.582A pdb=" N GLY B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.855A pdb=" N THR B 238 " --> pdb=" O ASN B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 388 through 392 removed outlier: 3.906A pdb=" N THR B 391 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 392 " --> pdb=" O GLY B 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 388 through 392' Processing helix chain 'B' and resid 402 through 422 removed outlier: 3.568A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.813A pdb=" N TRP B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 5.629A pdb=" N GLY B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 476 removed outlier: 3.775A pdb=" N ALA B 476 " --> pdb=" O MET B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 499 Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.913A pdb=" N SER C 86 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 235 through 238 removed outlier: 3.890A pdb=" N THR C 238 " --> pdb=" O ASN C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.944A pdb=" N THR C 391 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 392 " --> pdb=" O GLY C 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 388 through 392' Processing helix chain 'C' and resid 402 through 422 removed outlier: 3.642A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.718A pdb=" N TRP C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 427' Processing helix chain 'C' and resid 430 through 455 removed outlier: 5.140A pdb=" N GLY C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 475 Processing helix chain 'C' and resid 480 through 499 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 115 through 131 removed outlier: 3.676A pdb=" N TYR D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.602A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.577A pdb=" N VAL D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Proline residue: D 164 - end of helix removed outlier: 3.732A pdb=" N SER D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.589A pdb=" N GLN E 20 " --> pdb=" O THR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 131 removed outlier: 3.738A pdb=" N LEU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 148 through 167 Proline residue: E 164 - end of helix Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 115 through 131 Processing helix chain 'F' and resid 131 through 146 removed outlier: 3.577A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 167 Proline residue: F 164 - end of helix removed outlier: 3.678A pdb=" N SER F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.547A pdb=" N MET A 34 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE A 43 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A 142 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL A 45 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 140 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 47 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.547A pdb=" N MET A 34 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 4.076A pdb=" N THR A 187 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP A 293 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR A 185 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 96 removed outlier: 4.265A pdb=" N LYS A 118 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 67 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR A 120 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU A 65 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS A 122 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 63 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS A 124 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 61 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR A 126 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR A 59 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS A 128 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG A 57 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 58 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 96 removed outlier: 4.386A pdb=" N SER A 210 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 270 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 304 removed outlier: 7.243A pdb=" N GLY A 303 " --> pdb=" O ARG A 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.612A pdb=" N ALA A 316 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.627A pdb=" N GLU A 376 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 354 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AB2, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.847A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU B 138 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET B 48 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 136 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.847A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 20 through 25 removed outlier: 4.121A pdb=" N THR B 187 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP B 293 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 185 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 99 removed outlier: 4.009A pdb=" N ARG B 99 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 109 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 112 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 118 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR B 67 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 120 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B 65 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LYS B 122 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 63 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LYS B 124 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR B 61 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR B 126 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 59 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS B 128 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG B 57 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 90 through 99 removed outlier: 4.009A pdb=" N ARG B 99 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 109 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B 210 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 270 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AB8, first strand: chain 'B' and resid 303 through 304 removed outlier: 7.269A pdb=" N GLY B 303 " --> pdb=" O ARG B 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.544A pdb=" N ALA B 316 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 376 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 354 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 340 through 343 Processing sheet with id=AC2, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.531A pdb=" N MET C 34 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU C 138 " --> pdb=" O MET C 46 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N MET C 48 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 136 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.531A pdb=" N MET C 34 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 20 through 25 removed outlier: 4.086A pdb=" N THR C 187 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP C 293 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 185 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 90 through 99 removed outlier: 6.733A pdb=" N SER C 112 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP C 114 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 70 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS C 116 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 66 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU C 62 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS C 124 " --> pdb=" O CYS C 60 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS C 60 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR C 126 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 58 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LYS C 128 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL C 56 " --> pdb=" O LYS C 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 90 through 99 removed outlier: 4.379A pdb=" N SER C 210 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 270 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 240 through 242 Processing sheet with id=AC8, first strand: chain 'C' and resid 303 through 304 removed outlier: 7.188A pdb=" N GLY C 303 " --> pdb=" O ARG C 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 309 through 310 removed outlier: 3.501A pdb=" N ALA C 316 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 309 through 310 removed outlier: 3.535A pdb=" N GLU C 376 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 354 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 343 Processing sheet with id=AD3, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AD4, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AD5, first strand: chain 'D' and resid 48 through 53 removed outlier: 3.915A pdb=" N VAL D 74 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AD7, first strand: chain 'E' and resid 23 through 27 Processing sheet with id=AD8, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.942A pdb=" N VAL E 74 " --> pdb=" O CYS E 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 23 through 27 Processing sheet with id=AE2, first strand: chain 'F' and resid 48 through 53 removed outlier: 4.036A pdb=" N VAL F 74 " --> pdb=" O CYS F 53 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1932 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: 2.26 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4927 1.34 - 1.46: 3710 1.46 - 1.58: 6808 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 15589 Sorted by residual: bond pdb=" N ARG B 479 " pdb=" CA ARG B 479 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.63e+00 bond pdb=" C1 MAN K 5 " pdb=" O5 MAN K 5 " ideal model delta sigma weight residual 1.399 1.419 -0.020 2.00e-02 2.50e+03 9.54e-01 bond pdb=" C1 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.399 1.417 -0.018 2.00e-02 2.50e+03 8.36e-01 bond pdb=" CA ARG B 479 " pdb=" C ARG B 479 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.05e-01 bond pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.59e-01 ... (remaining 15584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 20775 1.73 - 3.46: 345 3.46 - 5.19: 43 5.19 - 6.92: 11 6.92 - 8.65: 1 Bond angle restraints: 21175 Sorted by residual: angle pdb=" C ARG C 477 " pdb=" N ASP C 478 " pdb=" CA ASP C 478 " ideal model delta sigma weight residual 121.54 127.73 -6.19 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C VAL A 91 " pdb=" N CYS A 92 " pdb=" CA CYS A 92 " ideal model delta sigma weight residual 121.64 116.31 5.33 1.70e+00 3.46e-01 9.85e+00 angle pdb=" C TRP B 426 " pdb=" N ASP B 427 " pdb=" CA ASP B 427 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.36e+00 angle pdb=" C TRP C 426 " pdb=" N ASP C 427 " pdb=" CA ASP C 427 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.24e+00 angle pdb=" C TRP A 426 " pdb=" N ASP A 427 " pdb=" CA ASP A 427 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.97e+00 ... (remaining 21170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.82: 8811 20.82 - 41.64: 582 41.64 - 62.45: 76 62.45 - 83.27: 28 83.27 - 104.09: 2 Dihedral angle restraints: 9499 sinusoidal: 3925 harmonic: 5574 Sorted by residual: dihedral pdb=" CB CYS B 3 " pdb=" SG CYS B 3 " pdb=" SG CYS B 30 " pdb=" CB CYS B 30 " ideal model delta sinusoidal sigma weight residual 93.00 148.24 -55.24 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual 93.00 145.90 -52.90 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual 93.00 142.32 -49.32 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 9496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1855 0.044 - 0.089: 493 0.089 - 0.133: 151 0.133 - 0.177: 8 0.177 - 0.221: 3 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.05 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 154 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" O3 BMA K 3 " both_signs ideal model delta sigma weight residual False 2.41 2.21 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2507 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 485 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C LEU B 485 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU B 485 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 486 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 17 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C THR D 17 " 0.020 2.00e-02 2.50e+03 pdb=" O THR D 17 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP D 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 74 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO B 75 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " -0.015 5.00e-02 4.00e+02 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3692 2.80 - 3.33: 15056 3.33 - 3.85: 25034 3.85 - 4.38: 27064 4.38 - 4.90: 46222 Nonbonded interactions: 117068 Sorted by model distance: nonbonded pdb=" CD1 TRP B 471 " pdb=" CE2 TRP B 471 " model vdw 2.277 2.784 nonbonded pdb=" CD1 TRP A 471 " pdb=" CE2 TRP A 471 " model vdw 2.277 2.784 nonbonded pdb=" O5 BMA L 3 " pdb=" O6 BMA L 3 " model vdw 2.416 2.432 nonbonded pdb=" O5 BMA J 3 " pdb=" O6 BMA J 3 " model vdw 2.436 2.432 nonbonded pdb=" O5 NAG J 2 " pdb=" O6 NAG J 2 " model vdw 2.450 2.432 ... (remaining 117063 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 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 470 or (resid 471 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE2 or name C \ E3 or name CZ2 or name CZ3 or name CH2)) or resid 472 through 499)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.230 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.002 0.037 15635 Z= 0.100 Angle : 0.556 8.653 21289 Z= 0.286 Chirality : 0.043 0.221 2510 Planarity : 0.003 0.031 2652 Dihedral : 13.394 104.090 5863 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 0.12 (0.19), residues: 1950 helix: 1.28 (0.24), residues: 489 sheet: 0.58 (0.23), residues: 522 loop : -0.84 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 94 TYR 0.014 0.001 TYR F 51 PHE 0.013 0.001 PHE B 43 TRP 0.009 0.001 TRP F 75 HIS 0.004 0.000 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (15589) covalent geometry : angle 0.54639 / 0.28 (21175) SS BOND : bond 0.00346 / 0.21 ( 24) SS BOND : angle 1.23950 / 0.81 ( 48) hydrogen bonds : bond 0.11438 / 7.58 ( 658) hydrogen bonds : angle 5.90790 / 4.09 ( 1932) link_ALPHA1-3 : bond 0.00623 / 0.30 ( 3) link_ALPHA1-3 : angle 1.93083 / 1.20 ( 9) link_ALPHA1-6 : bond 0.01025 / 0.49 ( 3) link_ALPHA1-6 : angle 2.31073 / 1.45 ( 9) link_BETA1-4 : bond 0.00510 / 0.24 ( 10) link_BETA1-4 : angle 1.48971 / 1.00 ( 30) link_NAG-ASN : bond 0.00153 / 0.08 ( 6) link_NAG-ASN : angle 1.19636 / 0.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9606 (mmtt) cc_final: 0.9229 (mmmm) REVERT: A 48 MET cc_start: 0.7901 (pmm) cc_final: 0.7587 (pmm) REVERT: A 133 GLU cc_start: 0.9363 (pm20) cc_final: 0.9097 (pm20) REVERT: A 172 GLN cc_start: 0.9308 (mp10) cc_final: 0.9024 (mp10) REVERT: A 180 MET cc_start: 0.8558 (mmm) cc_final: 0.7805 (tpp) REVERT: A 202 TYR cc_start: 0.8859 (m-80) cc_final: 0.8067 (m-80) REVERT: A 219 HIS cc_start: 0.9285 (m-70) cc_final: 0.8483 (m170) REVERT: A 255 LEU cc_start: 0.8496 (mt) cc_final: 0.8221 (mt) REVERT: A 348 ASP cc_start: 0.8583 (p0) cc_final: 0.8290 (p0) REVERT: A 417 ARG cc_start: 0.8592 (ppt170) cc_final: 0.7968 (ppt170) REVERT: A 421 LEU cc_start: 0.9595 (pp) cc_final: 0.9276 (pp) REVERT: A 426 TRP cc_start: 0.7394 (m100) cc_final: 0.6855 (m-10) REVERT: A 462 GLN cc_start: 0.9512 (mp10) cc_final: 0.9215 (mp10) REVERT: B 20 TRP cc_start: 0.8404 (p90) cc_final: 0.8162 (p90) REVERT: B 95 ASP cc_start: 0.8797 (t0) cc_final: 0.8559 (t0) REVERT: B 189 ASP cc_start: 0.9186 (t70) cc_final: 0.8790 (p0) REVERT: B 216 ASP cc_start: 0.8645 (p0) cc_final: 0.8362 (p0) REVERT: B 221 LEU cc_start: 0.9331 (mt) cc_final: 0.8798 (mt) REVERT: B 241 GLU cc_start: 0.8789 (tp30) cc_final: 0.8310 (tm-30) REVERT: B 246 HIS cc_start: 0.8594 (t-170) cc_final: 0.8200 (t70) REVERT: B 282 GLN cc_start: 0.9057 (mm110) cc_final: 0.8832 (mm-40) REVERT: B 292 LEU cc_start: 0.9488 (mt) cc_final: 0.9209 (mt) REVERT: B 298 LYS cc_start: 0.9101 (ptmt) cc_final: 0.8429 (ptpt) REVERT: B 304 MET cc_start: 0.8637 (tpt) cc_final: 0.8072 (tpt) REVERT: B 314 ASN cc_start: 0.9592 (t0) cc_final: 0.9304 (t0) REVERT: B 317 ASP cc_start: 0.8691 (t0) cc_final: 0.8449 (t0) REVERT: B 373 ILE cc_start: 0.9276 (mm) cc_final: 0.8994 (mm) REVERT: B 397 TRP cc_start: 0.9265 (t-100) cc_final: 0.8569 (t-100) REVERT: B 412 TRP cc_start: 0.8745 (t60) cc_final: 0.8434 (t60) REVERT: B 423 ASP cc_start: 0.8538 (m-30) cc_final: 0.8226 (t70) REVERT: B 492 LEU cc_start: 0.9633 (mt) cc_final: 0.9298 (mt) REVERT: B 495 LEU cc_start: 0.9338 (tt) cc_final: 0.9080 (mt) REVERT: C 23 LEU cc_start: 0.9116 (mt) cc_final: 0.8878 (mt) REVERT: C 42 ASP cc_start: 0.7232 (p0) cc_final: 0.6859 (p0) REVERT: C 43 PHE cc_start: 0.9511 (m-80) cc_final: 0.9309 (m-80) REVERT: C 93 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8891 (ttpp) REVERT: C 137 TYR cc_start: 0.8626 (m-80) cc_final: 0.7766 (m-80) REVERT: C 201 TYR cc_start: 0.8880 (m-10) cc_final: 0.8549 (m-10) REVERT: C 211 TRP cc_start: 0.8817 (m-10) cc_final: 0.8320 (m-10) REVERT: C 253 VAL cc_start: 0.8610 (p) cc_final: 0.8100 (t) REVERT: C 287 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8849 (tppt) REVERT: C 296 LYS cc_start: 0.9338 (pttt) cc_final: 0.9091 (pttm) REVERT: C 327 LEU cc_start: 0.8671 (mm) cc_final: 0.8454 (mm) REVERT: C 397 TRP cc_start: 0.9092 (t-100) cc_final: 0.8837 (t-100) REVERT: C 453 LEU cc_start: 0.9286 (pp) cc_final: 0.9075 (pp) REVERT: C 494 PHE cc_start: 0.9340 (t80) cc_final: 0.8946 (t80) REVERT: D 126 ASN cc_start: 0.9339 (m110) cc_final: 0.9087 (m110) REVERT: D 131 ASN cc_start: 0.8209 (p0) cc_final: 0.7944 (p0) REVERT: D 161 LEU cc_start: 0.8859 (mm) cc_final: 0.8596 (mm) REVERT: E 72 GLU cc_start: 0.8739 (tp30) cc_final: 0.8506 (tp30) REVERT: E 73 GLU cc_start: 0.8491 (tp30) cc_final: 0.8258 (tp30) REVERT: E 126 ASN cc_start: 0.8650 (m110) cc_final: 0.8355 (t0) REVERT: E 158 MET cc_start: 0.9067 (mmp) cc_final: 0.8741 (ptt) REVERT: F 78 TYR cc_start: 0.8502 (p90) cc_final: 0.8055 (p90) REVERT: F 84 MET cc_start: 0.8550 (ttt) cc_final: 0.8210 (tmm) REVERT: F 126 ASN cc_start: 0.9408 (m-40) cc_final: 0.9104 (t0) REVERT: F 131 ASN cc_start: 0.7629 (p0) cc_final: 0.7064 (p0) REVERT: F 155 PHE cc_start: 0.9132 (m-10) cc_final: 0.8926 (m-80) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.1119 time to fit residues: 109.2074 Evaluate side-chains 442 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 320 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 263 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 443 HIS C 144 HIS C 359 ASN C 443 HIS C 444 GLN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062876 restraints weight = 75555.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064760 restraints weight = 45420.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066073 restraints weight = 31993.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067022 restraints weight = 24894.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067678 restraints weight = 20703.642| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 15635 Z= 0.269 Angle : 0.754 10.170 21289 Z= 0.391 Chirality : 0.047 0.276 2510 Planarity : 0.005 0.061 2652 Dihedral : 8.453 103.194 2542 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.61 % Allowed : 6.63 % Favored : 92.76 % 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: -0.06 (0.19), residues: 1950 helix: 1.27 (0.24), residues: 489 sheet: 0.44 (0.23), residues: 486 loop : -0.97 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 417 TYR 0.024 0.003 TYR E 166 PHE 0.032 0.003 PHE C 379 TRP 0.025 0.002 TRP F 143 HIS 0.010 0.002 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (15589) covalent geometry : angle 0.74292 / 0.39 (21175) SS BOND : bond 0.00987 / 0.57 ( 24) SS BOND : angle 1.81311 / 1.00 ( 48) hydrogen bonds : bond 0.04039 / 2.65 ( 658) hydrogen bonds : angle 5.51172 / 3.80 ( 1932) link_ALPHA1-3 : bond 0.00686 / 0.33 ( 3) link_ALPHA1-3 : angle 3.16626 / 1.90 ( 9) link_ALPHA1-6 : bond 0.01229 / 0.59 ( 3) link_ALPHA1-6 : angle 2.11803 / 1.35 ( 9) link_BETA1-4 : bond 0.00517 / 0.23 ( 10) link_BETA1-4 : angle 1.57781 / 1.00 ( 30) link_NAG-ASN : bond 0.00471 / 0.26 ( 6) link_NAG-ASN : angle 1.55227 / 1.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 465 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9437 (tp) cc_final: 0.9190 (tp) REVERT: A 133 GLU cc_start: 0.9382 (pm20) cc_final: 0.8925 (pm20) REVERT: A 139 VAL cc_start: 0.9772 (t) cc_final: 0.9566 (t) REVERT: A 180 MET cc_start: 0.8854 (mmm) cc_final: 0.8043 (tpp) REVERT: A 202 TYR cc_start: 0.8952 (m-80) cc_final: 0.8432 (m-80) REVERT: A 292 LEU cc_start: 0.9438 (mt) cc_final: 0.9162 (mt) REVERT: A 348 ASP cc_start: 0.8701 (p0) cc_final: 0.8352 (p0) REVERT: A 372 MET cc_start: 0.8820 (mmp) cc_final: 0.8534 (mmm) REVERT: A 426 TRP cc_start: 0.7554 (m100) cc_final: 0.7025 (m-10) REVERT: B 20 TRP cc_start: 0.8396 (p90) cc_final: 0.7978 (p90) REVERT: B 88 LEU cc_start: 0.9437 (pt) cc_final: 0.9188 (pp) REVERT: B 137 TYR cc_start: 0.8770 (m-80) cc_final: 0.8551 (m-10) REVERT: B 182 GLU cc_start: 0.8225 (tp30) cc_final: 0.7543 (tp30) REVERT: B 189 ASP cc_start: 0.9313 (t70) cc_final: 0.8862 (p0) REVERT: B 193 ARG cc_start: 0.7937 (mpp-170) cc_final: 0.6871 (mpt180) REVERT: B 246 HIS cc_start: 0.8612 (t-170) cc_final: 0.8164 (t70) REVERT: B 293 ASP cc_start: 0.8563 (t70) cc_final: 0.8312 (t0) REVERT: B 298 LYS cc_start: 0.9238 (ptmt) cc_final: 0.8820 (tptt) REVERT: B 302 TYR cc_start: 0.7678 (m-10) cc_final: 0.7072 (m-80) REVERT: B 350 THR cc_start: 0.8999 (p) cc_final: 0.8782 (p) REVERT: B 383 TYR cc_start: 0.8278 (m-10) cc_final: 0.8042 (m-10) REVERT: B 396 HIS cc_start: 0.8776 (t-170) cc_final: 0.8411 (t-170) REVERT: B 417 ARG cc_start: 0.8920 (ptt90) cc_final: 0.8056 (ppt170) REVERT: C 20 TRP cc_start: 0.8916 (p90) cc_final: 0.8450 (p-90) REVERT: C 23 LEU cc_start: 0.9365 (mt) cc_final: 0.9147 (mt) REVERT: C 43 PHE cc_start: 0.9464 (m-80) cc_final: 0.9174 (m-80) REVERT: C 200 ASP cc_start: 0.8490 (p0) cc_final: 0.8242 (p0) REVERT: C 296 LYS cc_start: 0.9375 (pttt) cc_final: 0.9134 (pttm) REVERT: C 359 ASN cc_start: 0.8973 (t0) cc_final: 0.8747 (t0) REVERT: C 397 TRP cc_start: 0.9187 (t-100) cc_final: 0.8964 (t-100) REVERT: C 426 TRP cc_start: 0.8516 (m100) cc_final: 0.7653 (m-10) REVERT: C 494 PHE cc_start: 0.9358 (t80) cc_final: 0.9102 (t80) REVERT: D 126 ASN cc_start: 0.9282 (m110) cc_final: 0.9032 (m110) REVERT: D 157 ILE cc_start: 0.9107 (tt) cc_final: 0.8897 (tt) REVERT: D 161 LEU cc_start: 0.8837 (mm) cc_final: 0.8516 (mm) REVERT: E 40 ASP cc_start: 0.9046 (m-30) cc_final: 0.8644 (m-30) REVERT: E 72 GLU cc_start: 0.8767 (tp30) cc_final: 0.8561 (tp30) REVERT: E 78 TYR cc_start: 0.9360 (p90) cc_final: 0.8996 (p90) REVERT: E 83 ARG cc_start: 0.8441 (ppt170) cc_final: 0.8179 (ppt170) REVERT: E 125 GLU cc_start: 0.8856 (pp20) cc_final: 0.8652 (pp20) REVERT: E 126 ASN cc_start: 0.8455 (m110) cc_final: 0.8176 (m110) REVERT: E 130 ARG cc_start: 0.8796 (mmt90) cc_final: 0.8558 (mmp80) REVERT: E 158 MET cc_start: 0.9054 (mmp) cc_final: 0.8731 (ptt) REVERT: E 160 MET cc_start: 0.9205 (ttm) cc_final: 0.8972 (ttm) REVERT: F 78 TYR cc_start: 0.8640 (p90) cc_final: 0.8167 (p90) REVERT: F 89 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8188 (mtm110) REVERT: F 126 ASN cc_start: 0.9424 (m-40) cc_final: 0.9195 (t0) REVERT: F 155 PHE cc_start: 0.9196 (m-10) cc_final: 0.8955 (m-80) outliers start: 10 outliers final: 4 residues processed: 474 average time/residue: 0.1118 time to fit residues: 76.5890 Evaluate side-chains 391 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 184 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 HIS B 162 ASN B 263 HIS B 359 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 443 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS F 99 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062303 restraints weight = 74424.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064188 restraints weight = 44839.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065513 restraints weight = 31565.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.066452 restraints weight = 24503.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067107 restraints weight = 20397.193| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15635 Z= 0.204 Angle : 0.679 8.287 21289 Z= 0.355 Chirality : 0.047 0.277 2510 Planarity : 0.006 0.229 2652 Dihedral : 8.547 105.078 2542 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.37 % Allowed : 4.79 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1950 helix: 1.06 (0.23), residues: 507 sheet: 0.32 (0.24), residues: 492 loop : -0.98 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 451 TYR 0.025 0.002 TYR A 137 PHE 0.027 0.002 PHE C 454 TRP 0.025 0.002 TRP F 143 HIS 0.020 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (15589) covalent geometry : angle 0.66391 / 0.35 (21175) SS BOND : bond 0.00427 / 0.27 ( 24) SS BOND : angle 2.37039 / 1.35 ( 48) hydrogen bonds : bond 0.03796 / 2.50 ( 658) hydrogen bonds : angle 5.30235 / 3.68 ( 1932) link_ALPHA1-3 : bond 0.00669 / 0.32 ( 3) link_ALPHA1-3 : angle 2.70360 / 1.64 ( 9) link_ALPHA1-6 : bond 0.01247 / 0.60 ( 3) link_ALPHA1-6 : angle 2.09668 / 1.33 ( 9) link_BETA1-4 : bond 0.00534 / 0.25 ( 10) link_BETA1-4 : angle 1.46596 / 0.94 ( 30) link_NAG-ASN : bond 0.00196 / 0.10 ( 6) link_NAG-ASN : angle 1.33777 / 0.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 462 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9445 (tp) cc_final: 0.9151 (tp) REVERT: A 26 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 30 CYS cc_start: 0.4072 (OUTLIER) cc_final: 0.0885 (p) REVERT: A 133 GLU cc_start: 0.9351 (pm20) cc_final: 0.8828 (pm20) REVERT: A 180 MET cc_start: 0.8893 (mmm) cc_final: 0.8258 (tpp) REVERT: A 202 TYR cc_start: 0.8925 (m-80) cc_final: 0.8417 (m-80) REVERT: A 302 TYR cc_start: 0.8570 (m-10) cc_final: 0.8128 (m-10) REVERT: A 348 ASP cc_start: 0.8680 (p0) cc_final: 0.8358 (p0) REVERT: A 426 TRP cc_start: 0.7574 (m100) cc_final: 0.7180 (m-10) REVERT: A 440 LYS cc_start: 0.9592 (mtmm) cc_final: 0.9202 (mtmm) REVERT: B 20 TRP cc_start: 0.8380 (p90) cc_final: 0.8153 (p90) REVERT: B 88 LEU cc_start: 0.9413 (pt) cc_final: 0.9200 (pp) REVERT: B 137 TYR cc_start: 0.8636 (m-80) cc_final: 0.8420 (m-80) REVERT: B 182 GLU cc_start: 0.7980 (tp30) cc_final: 0.7225 (tp30) REVERT: B 189 ASP cc_start: 0.9273 (t70) cc_final: 0.8929 (p0) REVERT: B 193 ARG cc_start: 0.7984 (mpp-170) cc_final: 0.6910 (mpt180) REVERT: B 246 HIS cc_start: 0.8642 (t-170) cc_final: 0.8247 (t70) REVERT: B 292 LEU cc_start: 0.9561 (mt) cc_final: 0.9340 (mt) REVERT: B 293 ASP cc_start: 0.8683 (t70) cc_final: 0.8435 (t0) REVERT: B 294 LYS cc_start: 0.9582 (mmpt) cc_final: 0.9099 (mmmt) REVERT: B 298 LYS cc_start: 0.9298 (ptmt) cc_final: 0.8777 (tptt) REVERT: B 302 TYR cc_start: 0.7780 (m-10) cc_final: 0.7393 (m-80) REVERT: B 350 THR cc_start: 0.9030 (p) cc_final: 0.8795 (p) REVERT: B 383 TYR cc_start: 0.8460 (m-10) cc_final: 0.8148 (m-10) REVERT: B 396 HIS cc_start: 0.8788 (t-170) cc_final: 0.8494 (t-170) REVERT: B 399 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8905 (ptpp) REVERT: C 20 TRP cc_start: 0.8848 (p90) cc_final: 0.8387 (p-90) REVERT: C 95 ASP cc_start: 0.8150 (t0) cc_final: 0.7928 (t0) REVERT: C 137 TYR cc_start: 0.8678 (m-80) cc_final: 0.7622 (m-80) REVERT: C 180 MET cc_start: 0.9067 (mmt) cc_final: 0.8573 (mpp) REVERT: C 296 LYS cc_start: 0.9392 (pttt) cc_final: 0.9134 (pttm) REVERT: C 345 ASN cc_start: 0.8990 (p0) cc_final: 0.8162 (p0) REVERT: C 397 TRP cc_start: 0.9214 (t-100) cc_final: 0.8973 (t-100) REVERT: C 423 ASP cc_start: 0.7412 (m-30) cc_final: 0.7101 (m-30) REVERT: C 426 TRP cc_start: 0.8523 (m100) cc_final: 0.7890 (m-10) REVERT: C 457 MET cc_start: 0.8340 (ttp) cc_final: 0.7976 (ttt) REVERT: C 494 PHE cc_start: 0.9319 (t80) cc_final: 0.9098 (t80) REVERT: D 126 ASN cc_start: 0.9292 (m110) cc_final: 0.9036 (m110) REVERT: E 14 ILE cc_start: 0.9033 (tp) cc_final: 0.8277 (tp) REVERT: E 72 GLU cc_start: 0.8798 (tp30) cc_final: 0.8570 (tp30) REVERT: E 78 TYR cc_start: 0.9385 (p90) cc_final: 0.8801 (p90) REVERT: E 83 ARG cc_start: 0.8279 (ppt170) cc_final: 0.8022 (ppt170) REVERT: E 97 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6537 (tp-100) REVERT: E 125 GLU cc_start: 0.8873 (pp20) cc_final: 0.8653 (pp20) REVERT: E 158 MET cc_start: 0.9067 (mmp) cc_final: 0.8712 (ptt) REVERT: E 160 MET cc_start: 0.9199 (ttm) cc_final: 0.8967 (ttm) REVERT: F 78 TYR cc_start: 0.8623 (p90) cc_final: 0.8170 (p90) REVERT: F 89 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8334 (mtm110) REVERT: F 155 PHE cc_start: 0.9098 (m-10) cc_final: 0.8897 (m-80) outliers start: 6 outliers final: 1 residues processed: 468 average time/residue: 0.1219 time to fit residues: 82.6281 Evaluate side-chains 395 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 392 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 263 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059839 restraints weight = 75600.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061684 restraints weight = 44731.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062970 restraints weight = 31211.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063888 restraints weight = 24142.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064529 restraints weight = 20030.717| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15635 Z= 0.261 Angle : 0.737 8.673 21289 Z= 0.384 Chirality : 0.048 0.294 2510 Planarity : 0.005 0.120 2652 Dihedral : 8.750 105.480 2542 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.18 % Allowed : 5.34 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.47 (0.19), residues: 1950 helix: 0.83 (0.23), residues: 504 sheet: 0.11 (0.23), residues: 488 loop : -1.15 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 37 TYR 0.021 0.002 TYR F 51 PHE 0.021 0.002 PHE B 450 TRP 0.021 0.002 TRP D 127 HIS 0.011 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (15589) covalent geometry : angle 0.72422 / 0.38 (21175) SS BOND : bond 0.00335 / 0.18 ( 24) SS BOND : angle 2.17615 / 1.23 ( 48) hydrogen bonds : bond 0.03892 / 2.56 ( 658) hydrogen bonds : angle 5.43646 / 3.78 ( 1932) link_ALPHA1-3 : bond 0.00695 / 0.33 ( 3) link_ALPHA1-3 : angle 3.03607 / 1.81 ( 9) link_ALPHA1-6 : bond 0.01372 / 0.66 ( 3) link_ALPHA1-6 : angle 2.09759 / 1.33 ( 9) link_BETA1-4 : bond 0.00516 / 0.23 ( 10) link_BETA1-4 : angle 1.51620 / 0.97 ( 30) link_NAG-ASN : bond 0.00395 / 0.21 ( 6) link_NAG-ASN : angle 1.53179 / 1.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 438 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9424 (tp) cc_final: 0.9131 (tp) REVERT: A 95 ASP cc_start: 0.8847 (t70) cc_final: 0.8555 (t0) REVERT: A 133 GLU cc_start: 0.9362 (pm20) cc_final: 0.8811 (pm20) REVERT: A 139 VAL cc_start: 0.9790 (t) cc_final: 0.9543 (t) REVERT: A 180 MET cc_start: 0.8909 (mmm) cc_final: 0.8309 (tpp) REVERT: A 202 TYR cc_start: 0.8987 (m-80) cc_final: 0.8375 (m-80) REVERT: A 348 ASP cc_start: 0.8728 (p0) cc_final: 0.8425 (p0) REVERT: A 372 MET cc_start: 0.8992 (mmp) cc_final: 0.8692 (mmm) REVERT: A 426 TRP cc_start: 0.7683 (m100) cc_final: 0.7221 (m-10) REVERT: A 446 PHE cc_start: 0.8914 (m-10) cc_final: 0.8651 (m-80) REVERT: B 20 TRP cc_start: 0.8540 (p90) cc_final: 0.8288 (p90) REVERT: B 137 TYR cc_start: 0.8728 (m-80) cc_final: 0.8516 (m-80) REVERT: B 182 GLU cc_start: 0.8242 (tp30) cc_final: 0.7934 (tp30) REVERT: B 189 ASP cc_start: 0.9248 (t70) cc_final: 0.8988 (p0) REVERT: B 193 ARG cc_start: 0.8124 (mpp-170) cc_final: 0.6854 (mpt180) REVERT: B 246 HIS cc_start: 0.8711 (t-170) cc_final: 0.8310 (t70) REVERT: B 279 LEU cc_start: 0.9194 (tp) cc_final: 0.8973 (pt) REVERT: B 293 ASP cc_start: 0.8797 (t70) cc_final: 0.8545 (t0) REVERT: B 294 LYS cc_start: 0.9631 (mmpt) cc_final: 0.9158 (mmmt) REVERT: B 298 LYS cc_start: 0.9360 (ptmt) cc_final: 0.9152 (tptt) REVERT: B 383 TYR cc_start: 0.8468 (m-10) cc_final: 0.8211 (m-10) REVERT: B 396 HIS cc_start: 0.8837 (t-170) cc_final: 0.8551 (t-170) REVERT: B 423 ASP cc_start: 0.9305 (p0) cc_final: 0.9009 (p0) REVERT: B 426 TRP cc_start: 0.8204 (m100) cc_final: 0.7574 (m-10) REVERT: C 20 TRP cc_start: 0.8919 (p90) cc_final: 0.8500 (p-90) REVERT: C 23 LEU cc_start: 0.9277 (mt) cc_final: 0.8986 (mt) REVERT: C 43 PHE cc_start: 0.9372 (m-80) cc_final: 0.9109 (m-10) REVERT: C 137 TYR cc_start: 0.8760 (m-80) cc_final: 0.7854 (m-80) REVERT: C 155 TYR cc_start: 0.7358 (t80) cc_final: 0.7026 (t80) REVERT: C 296 LYS cc_start: 0.9368 (pttt) cc_final: 0.9122 (pttm) REVERT: C 345 ASN cc_start: 0.8906 (p0) cc_final: 0.8493 (p0) REVERT: C 385 VAL cc_start: 0.9567 (p) cc_final: 0.9324 (p) REVERT: C 395 TYR cc_start: 0.9066 (t80) cc_final: 0.8706 (t80) REVERT: C 418 LEU cc_start: 0.9448 (mt) cc_final: 0.9235 (mt) REVERT: C 423 ASP cc_start: 0.7461 (m-30) cc_final: 0.7046 (m-30) REVERT: C 426 TRP cc_start: 0.8538 (m100) cc_final: 0.7912 (m-10) REVERT: C 457 MET cc_start: 0.8229 (ttp) cc_final: 0.7873 (ttt) REVERT: C 472 MET cc_start: 0.9140 (mmm) cc_final: 0.8868 (mmm) REVERT: C 494 PHE cc_start: 0.9340 (t80) cc_final: 0.9139 (t80) REVERT: D 120 TYR cc_start: 0.8477 (m-10) cc_final: 0.8241 (m-80) REVERT: D 123 LYS cc_start: 0.9742 (ttmm) cc_final: 0.9494 (mtmm) REVERT: D 161 LEU cc_start: 0.8945 (mm) cc_final: 0.8709 (mm) REVERT: E 37 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7092 (tpp-160) REVERT: E 66 ASP cc_start: 0.7792 (p0) cc_final: 0.7586 (p0) REVERT: E 78 TYR cc_start: 0.9399 (p90) cc_final: 0.9044 (p90) REVERT: E 83 ARG cc_start: 0.8316 (ppt170) cc_final: 0.8035 (ppt170) REVERT: E 126 ASN cc_start: 0.8045 (m110) cc_final: 0.7713 (m110) REVERT: E 127 TRP cc_start: 0.9204 (t60) cc_final: 0.8899 (t60) REVERT: E 130 ARG cc_start: 0.8752 (mmt90) cc_final: 0.8466 (mmp80) REVERT: E 158 MET cc_start: 0.9098 (mmp) cc_final: 0.8732 (ptt) REVERT: E 160 MET cc_start: 0.9209 (ttm) cc_final: 0.8978 (ttm) REVERT: F 78 TYR cc_start: 0.8630 (p90) cc_final: 0.8218 (p90) REVERT: F 89 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8450 (mtm110) outliers start: 3 outliers final: 2 residues processed: 440 average time/residue: 0.1186 time to fit residues: 75.1258 Evaluate side-chains 377 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 128 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060960 restraints weight = 73596.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062864 restraints weight = 43262.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064188 restraints weight = 30055.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065124 restraints weight = 23191.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065793 restraints weight = 19261.980| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15635 Z= 0.153 Angle : 0.692 9.298 21289 Z= 0.354 Chirality : 0.047 0.299 2510 Planarity : 0.004 0.087 2652 Dihedral : 8.646 104.464 2542 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.30 (0.19), residues: 1950 helix: 0.95 (0.23), residues: 501 sheet: 0.16 (0.23), residues: 512 loop : -1.01 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 451 TYR 0.017 0.002 TYR F 51 PHE 0.032 0.002 PHE F 155 TRP 0.017 0.001 TRP F 127 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (15589) covalent geometry : angle 0.68102 / 0.35 (21175) SS BOND : bond 0.00445 / 0.26 ( 24) SS BOND : angle 1.86341 / 1.07 ( 48) hydrogen bonds : bond 0.03501 / 2.30 ( 658) hydrogen bonds : angle 5.24991 / 3.64 ( 1932) link_ALPHA1-3 : bond 0.00752 / 0.36 ( 3) link_ALPHA1-3 : angle 2.80162 / 1.70 ( 9) link_ALPHA1-6 : bond 0.01200 / 0.58 ( 3) link_ALPHA1-6 : angle 2.01666 / 1.29 ( 9) link_BETA1-4 : bond 0.00523 / 0.25 ( 10) link_BETA1-4 : angle 1.46045 / 0.95 ( 30) link_NAG-ASN : bond 0.00156 / 0.09 ( 6) link_NAG-ASN : angle 1.40827 / 0.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9456 (tp) cc_final: 0.9172 (tp) REVERT: A 133 GLU cc_start: 0.9407 (pm20) cc_final: 0.8864 (pm20) REVERT: A 139 VAL cc_start: 0.9810 (t) cc_final: 0.9552 (t) REVERT: A 180 MET cc_start: 0.8864 (mmm) cc_final: 0.8075 (tpp) REVERT: A 202 TYR cc_start: 0.8910 (m-80) cc_final: 0.8264 (m-80) REVERT: A 348 ASP cc_start: 0.8720 (p0) cc_final: 0.8421 (p0) REVERT: A 372 MET cc_start: 0.8894 (mmp) cc_final: 0.8607 (mmm) REVERT: A 426 TRP cc_start: 0.7637 (m100) cc_final: 0.7156 (m-10) REVERT: A 440 LYS cc_start: 0.9585 (mtmm) cc_final: 0.9209 (mtmm) REVERT: A 446 PHE cc_start: 0.8850 (m-10) cc_final: 0.8527 (m-80) REVERT: A 472 MET cc_start: 0.8724 (ppp) cc_final: 0.8509 (ppp) REVERT: B 20 TRP cc_start: 0.8467 (p90) cc_final: 0.8267 (p90) REVERT: B 95 ASP cc_start: 0.8737 (t0) cc_final: 0.8533 (t0) REVERT: B 137 TYR cc_start: 0.8743 (m-80) cc_final: 0.8536 (m-80) REVERT: B 189 ASP cc_start: 0.9172 (t70) cc_final: 0.8939 (p0) REVERT: B 246 HIS cc_start: 0.8625 (t-170) cc_final: 0.8223 (t70) REVERT: B 293 ASP cc_start: 0.8791 (t70) cc_final: 0.8575 (t0) REVERT: B 294 LYS cc_start: 0.9647 (mmpt) cc_final: 0.9162 (mmmt) REVERT: B 350 THR cc_start: 0.8917 (p) cc_final: 0.8677 (p) REVERT: B 383 TYR cc_start: 0.8548 (m-80) cc_final: 0.8334 (m-10) REVERT: B 423 ASP cc_start: 0.9299 (p0) cc_final: 0.8982 (p0) REVERT: B 426 TRP cc_start: 0.8207 (m100) cc_final: 0.7716 (m-10) REVERT: B 457 MET cc_start: 0.8288 (pmm) cc_final: 0.8067 (pmm) REVERT: C 20 TRP cc_start: 0.8893 (p90) cc_final: 0.8625 (p-90) REVERT: C 23 LEU cc_start: 0.9208 (mt) cc_final: 0.9003 (mt) REVERT: C 43 PHE cc_start: 0.9406 (m-80) cc_final: 0.9146 (m-10) REVERT: C 95 ASP cc_start: 0.8012 (t70) cc_final: 0.7737 (t0) REVERT: C 137 TYR cc_start: 0.8749 (m-80) cc_final: 0.8023 (m-80) REVERT: C 155 TYR cc_start: 0.7303 (t80) cc_final: 0.6972 (t80) REVERT: C 180 MET cc_start: 0.9135 (mmt) cc_final: 0.8551 (mpp) REVERT: C 201 TYR cc_start: 0.9122 (m-80) cc_final: 0.8856 (m-80) REVERT: C 296 LYS cc_start: 0.9334 (pttt) cc_final: 0.9079 (pttm) REVERT: C 426 TRP cc_start: 0.8516 (m100) cc_final: 0.7629 (m-10) REVERT: C 457 MET cc_start: 0.8311 (ttp) cc_final: 0.7867 (ttt) REVERT: C 472 MET cc_start: 0.9116 (mmm) cc_final: 0.8826 (mmm) REVERT: C 494 PHE cc_start: 0.9330 (t80) cc_final: 0.9118 (t80) REVERT: D 120 TYR cc_start: 0.8486 (m-10) cc_final: 0.8165 (m-80) REVERT: D 123 LYS cc_start: 0.9746 (ttmm) cc_final: 0.9511 (mtmm) REVERT: D 126 ASN cc_start: 0.9301 (m110) cc_final: 0.9050 (m110) REVERT: D 161 LEU cc_start: 0.8865 (mm) cc_final: 0.8654 (mm) REVERT: E 66 ASP cc_start: 0.7683 (p0) cc_final: 0.7469 (p0) REVERT: E 78 TYR cc_start: 0.9383 (p90) cc_final: 0.8964 (p90) REVERT: E 83 ARG cc_start: 0.8338 (ppt170) cc_final: 0.8018 (ppt170) REVERT: E 127 TRP cc_start: 0.9219 (t60) cc_final: 0.8934 (t60) REVERT: E 158 MET cc_start: 0.9115 (mmp) cc_final: 0.8757 (ptt) REVERT: E 160 MET cc_start: 0.9195 (ttm) cc_final: 0.8968 (ttm) REVERT: F 78 TYR cc_start: 0.8578 (p90) cc_final: 0.8194 (p90) REVERT: F 89 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8447 (mtm110) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1308 time to fit residues: 84.6249 Evaluate side-chains 376 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 171 optimal weight: 40.0000 chunk 191 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 263 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.059881 restraints weight = 74482.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061757 restraints weight = 43818.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063076 restraints weight = 30532.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064014 restraints weight = 23551.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064635 restraints weight = 19507.145| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15635 Z= 0.203 Angle : 0.729 15.028 21289 Z= 0.372 Chirality : 0.048 0.279 2510 Planarity : 0.005 0.128 2652 Dihedral : 8.695 104.329 2542 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.35 (0.19), residues: 1950 helix: 0.94 (0.23), residues: 501 sheet: 0.09 (0.23), residues: 518 loop : -1.05 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 193 TYR 0.020 0.002 TYR A 137 PHE 0.030 0.002 PHE F 155 TRP 0.019 0.002 TRP F 143 HIS 0.013 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (15589) covalent geometry : angle 0.71834 / 0.37 (21175) SS BOND : bond 0.00403 / 0.22 ( 24) SS BOND : angle 1.86047 / 1.08 ( 48) hydrogen bonds : bond 0.03644 / 2.39 ( 658) hydrogen bonds : angle 5.31910 / 3.70 ( 1932) link_ALPHA1-3 : bond 0.00714 / 0.34 ( 3) link_ALPHA1-3 : angle 2.95935 / 1.79 ( 9) link_ALPHA1-6 : bond 0.01233 / 0.59 ( 3) link_ALPHA1-6 : angle 2.00253 / 1.28 ( 9) link_BETA1-4 : bond 0.00512 / 0.23 ( 10) link_BETA1-4 : angle 1.49004 / 0.96 ( 30) link_NAG-ASN : bond 0.00301 / 0.16 ( 6) link_NAG-ASN : angle 1.52047 / 1.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9449 (tp) cc_final: 0.9158 (tp) REVERT: A 95 ASP cc_start: 0.8777 (t70) cc_final: 0.8563 (t70) REVERT: A 133 GLU cc_start: 0.9399 (pm20) cc_final: 0.8859 (pm20) REVERT: A 137 TYR cc_start: 0.9274 (m-80) cc_final: 0.9055 (m-80) REVERT: A 139 VAL cc_start: 0.9753 (t) cc_final: 0.9481 (t) REVERT: A 180 MET cc_start: 0.8883 (mmm) cc_final: 0.8132 (tpp) REVERT: A 202 TYR cc_start: 0.8937 (m-80) cc_final: 0.8327 (m-80) REVERT: A 348 ASP cc_start: 0.8695 (p0) cc_final: 0.8395 (p0) REVERT: A 372 MET cc_start: 0.8869 (mmp) cc_final: 0.8661 (mmm) REVERT: A 426 TRP cc_start: 0.7681 (m100) cc_final: 0.7192 (m-10) REVERT: A 440 LYS cc_start: 0.9590 (mtmm) cc_final: 0.9263 (mtmm) REVERT: A 446 PHE cc_start: 0.8932 (m-10) cc_final: 0.8593 (m-80) REVERT: B 20 TRP cc_start: 0.8535 (p90) cc_final: 0.8280 (p90) REVERT: B 137 TYR cc_start: 0.8776 (m-80) cc_final: 0.8554 (m-80) REVERT: B 189 ASP cc_start: 0.9146 (t70) cc_final: 0.8902 (p0) REVERT: B 246 HIS cc_start: 0.8643 (t-170) cc_final: 0.8206 (t70) REVERT: B 287 LYS cc_start: 0.9191 (ttmm) cc_final: 0.8933 (ttmm) REVERT: B 294 LYS cc_start: 0.9677 (mmpt) cc_final: 0.9226 (mmmt) REVERT: B 350 THR cc_start: 0.8877 (p) cc_final: 0.8610 (p) REVERT: B 383 TYR cc_start: 0.8642 (m-80) cc_final: 0.8385 (m-10) REVERT: B 423 ASP cc_start: 0.9305 (p0) cc_final: 0.8990 (p0) REVERT: B 426 TRP cc_start: 0.8238 (m100) cc_final: 0.7809 (m-10) REVERT: B 492 LEU cc_start: 0.9694 (mt) cc_final: 0.9463 (mt) REVERT: C 20 TRP cc_start: 0.8692 (p90) cc_final: 0.8348 (p-90) REVERT: C 43 PHE cc_start: 0.9426 (m-80) cc_final: 0.9198 (m-10) REVERT: C 95 ASP cc_start: 0.8070 (t70) cc_final: 0.7847 (t0) REVERT: C 155 TYR cc_start: 0.7219 (t80) cc_final: 0.6936 (t80) REVERT: C 180 MET cc_start: 0.9119 (mmt) cc_final: 0.8679 (mpp) REVERT: C 296 LYS cc_start: 0.9328 (pttt) cc_final: 0.9067 (pttm) REVERT: C 426 TRP cc_start: 0.8462 (m100) cc_final: 0.7542 (m-10) REVERT: C 457 MET cc_start: 0.8350 (ttp) cc_final: 0.7969 (ttt) REVERT: D 48 ASP cc_start: 0.8540 (p0) cc_final: 0.7463 (m-30) REVERT: D 120 TYR cc_start: 0.8538 (m-10) cc_final: 0.8204 (m-80) REVERT: D 123 LYS cc_start: 0.9744 (ttmm) cc_final: 0.9507 (mtmm) REVERT: D 126 ASN cc_start: 0.9298 (m110) cc_final: 0.9023 (m110) REVERT: D 161 LEU cc_start: 0.8847 (mm) cc_final: 0.8575 (mm) REVERT: E 78 TYR cc_start: 0.9412 (p90) cc_final: 0.8950 (p90) REVERT: E 83 ARG cc_start: 0.8373 (ppt170) cc_final: 0.8048 (ppt170) REVERT: E 127 TRP cc_start: 0.9216 (t60) cc_final: 0.8926 (t60) REVERT: E 158 MET cc_start: 0.9104 (mmp) cc_final: 0.8734 (ptt) REVERT: E 160 MET cc_start: 0.9179 (ttm) cc_final: 0.8945 (ttm) REVERT: F 78 TYR cc_start: 0.8600 (p90) cc_final: 0.8208 (p90) REVERT: F 89 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8384 (mtm110) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.1232 time to fit residues: 77.7500 Evaluate side-chains 364 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 187 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 162 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN E 131 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060465 restraints weight = 74199.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062302 restraints weight = 44533.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063580 restraints weight = 31384.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064465 restraints weight = 24507.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065099 restraints weight = 20584.987| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15635 Z= 0.169 Angle : 0.709 12.527 21289 Z= 0.360 Chirality : 0.048 0.291 2510 Planarity : 0.004 0.099 2652 Dihedral : 8.657 103.535 2542 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.19), residues: 1950 helix: 1.01 (0.23), residues: 501 sheet: 0.07 (0.23), residues: 516 loop : -1.04 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 451 TYR 0.017 0.002 TYR F 51 PHE 0.032 0.002 PHE F 155 TRP 0.019 0.002 TRP F 127 HIS 0.011 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (15589) covalent geometry : angle 0.69796 / 0.36 (21175) SS BOND : bond 0.00515 / 0.30 ( 24) SS BOND : angle 1.87065 / 1.11 ( 48) hydrogen bonds : bond 0.03498 / 2.28 ( 658) hydrogen bonds : angle 5.27442 / 3.65 ( 1932) link_ALPHA1-3 : bond 0.00740 / 0.35 ( 3) link_ALPHA1-3 : angle 2.87788 / 1.75 ( 9) link_ALPHA1-6 : bond 0.01233 / 0.59 ( 3) link_ALPHA1-6 : angle 1.97545 / 1.27 ( 9) link_BETA1-4 : bond 0.00522 / 0.24 ( 10) link_BETA1-4 : angle 1.45674 / 0.94 ( 30) link_NAG-ASN : bond 0.00237 / 0.13 ( 6) link_NAG-ASN : angle 1.51257 / 1.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9456 (tp) cc_final: 0.9162 (tp) REVERT: A 95 ASP cc_start: 0.8726 (t70) cc_final: 0.8522 (t70) REVERT: A 133 GLU cc_start: 0.9397 (pm20) cc_final: 0.8845 (pm20) REVERT: A 137 TYR cc_start: 0.9341 (m-80) cc_final: 0.8993 (m-10) REVERT: A 139 VAL cc_start: 0.9759 (t) cc_final: 0.9506 (t) REVERT: A 180 MET cc_start: 0.8907 (mmm) cc_final: 0.8155 (tpp) REVERT: A 202 TYR cc_start: 0.8886 (m-80) cc_final: 0.8271 (m-80) REVERT: A 348 ASP cc_start: 0.8640 (p0) cc_final: 0.8306 (p0) REVERT: A 426 TRP cc_start: 0.7617 (m100) cc_final: 0.7082 (m-10) REVERT: A 440 LYS cc_start: 0.9565 (mtmm) cc_final: 0.9197 (mtmm) REVERT: A 446 PHE cc_start: 0.8922 (m-10) cc_final: 0.8534 (m-80) REVERT: B 20 TRP cc_start: 0.8505 (p90) cc_final: 0.8247 (p90) REVERT: B 95 ASP cc_start: 0.8927 (t0) cc_final: 0.8698 (t0) REVERT: B 246 HIS cc_start: 0.8612 (t-170) cc_final: 0.8183 (t70) REVERT: B 287 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8911 (ttmm) REVERT: B 294 LYS cc_start: 0.9654 (mmpt) cc_final: 0.9228 (mmmt) REVERT: B 350 THR cc_start: 0.8875 (p) cc_final: 0.8606 (p) REVERT: B 383 TYR cc_start: 0.8681 (m-80) cc_final: 0.8332 (m-10) REVERT: B 423 ASP cc_start: 0.9328 (p0) cc_final: 0.9091 (p0) REVERT: B 426 TRP cc_start: 0.8283 (m100) cc_final: 0.7714 (m-10) REVERT: B 462 GLN cc_start: 0.9465 (mp10) cc_final: 0.9229 (mp-120) REVERT: B 492 LEU cc_start: 0.9691 (mt) cc_final: 0.9453 (mt) REVERT: C 20 TRP cc_start: 0.8720 (p90) cc_final: 0.8358 (p-90) REVERT: C 23 LEU cc_start: 0.9244 (mt) cc_final: 0.8983 (mt) REVERT: C 43 PHE cc_start: 0.9447 (m-80) cc_final: 0.9223 (m-10) REVERT: C 95 ASP cc_start: 0.7996 (t70) cc_final: 0.7756 (t70) REVERT: C 162 ASN cc_start: 0.8712 (t160) cc_final: 0.7522 (p0) REVERT: C 180 MET cc_start: 0.8968 (mmt) cc_final: 0.8544 (mpp) REVERT: C 287 LYS cc_start: 0.8805 (tppt) cc_final: 0.8466 (tppt) REVERT: C 296 LYS cc_start: 0.9326 (pttt) cc_final: 0.9046 (pttm) REVERT: C 345 ASN cc_start: 0.8870 (p0) cc_final: 0.8412 (p0) REVERT: C 385 VAL cc_start: 0.9422 (p) cc_final: 0.9218 (p) REVERT: C 418 LEU cc_start: 0.9434 (mm) cc_final: 0.9192 (mm) REVERT: C 426 TRP cc_start: 0.8460 (m100) cc_final: 0.7550 (m-10) REVERT: C 494 PHE cc_start: 0.9381 (t80) cc_final: 0.9068 (t80) REVERT: D 48 ASP cc_start: 0.8581 (p0) cc_final: 0.7688 (m-30) REVERT: D 120 TYR cc_start: 0.8577 (m-10) cc_final: 0.8216 (m-80) REVERT: D 123 LYS cc_start: 0.9743 (ttmm) cc_final: 0.9497 (mtmm) REVERT: D 126 ASN cc_start: 0.9329 (m110) cc_final: 0.9059 (m110) REVERT: D 157 ILE cc_start: 0.9119 (tt) cc_final: 0.8883 (tt) REVERT: D 161 LEU cc_start: 0.8908 (mm) cc_final: 0.8560 (mm) REVERT: E 78 TYR cc_start: 0.9440 (p90) cc_final: 0.8982 (p90) REVERT: E 83 ARG cc_start: 0.8339 (ppt170) cc_final: 0.7993 (ppt170) REVERT: E 130 ARG cc_start: 0.8783 (mmt90) cc_final: 0.8417 (mmp80) REVERT: E 158 MET cc_start: 0.9101 (mmp) cc_final: 0.8733 (ptt) REVERT: E 160 MET cc_start: 0.9182 (ttm) cc_final: 0.8955 (ttm) REVERT: F 78 TYR cc_start: 0.8585 (p90) cc_final: 0.8201 (p90) REVERT: F 89 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8374 (mtm110) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.1106 time to fit residues: 69.2053 Evaluate side-chains 369 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 47 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 263 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060601 restraints weight = 72343.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062448 restraints weight = 43372.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063736 restraints weight = 30461.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064645 restraints weight = 23669.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065287 restraints weight = 19746.021| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15635 Z= 0.168 Angle : 0.728 11.200 21289 Z= 0.370 Chirality : 0.048 0.276 2510 Planarity : 0.004 0.088 2652 Dihedral : 8.672 102.788 2542 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.39 (0.19), residues: 1950 helix: 0.88 (0.23), residues: 501 sheet: 0.01 (0.23), residues: 516 loop : -1.01 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 417 TYR 0.032 0.002 TYR B 137 PHE 0.047 0.002 PHE C 454 TRP 0.022 0.002 TRP E 127 HIS 0.015 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (15589) covalent geometry : angle 0.71696 / 0.37 (21175) SS BOND : bond 0.00814 / 0.46 ( 24) SS BOND : angle 1.89401 / 1.11 ( 48) hydrogen bonds : bond 0.03655 / 2.37 ( 658) hydrogen bonds : angle 5.34228 / 3.69 ( 1932) link_ALPHA1-3 : bond 0.00764 / 0.36 ( 3) link_ALPHA1-3 : angle 2.83984 / 1.73 ( 9) link_ALPHA1-6 : bond 0.01247 / 0.60 ( 3) link_ALPHA1-6 : angle 1.97940 / 1.27 ( 9) link_BETA1-4 : bond 0.00535 / 0.25 ( 10) link_BETA1-4 : angle 1.46693 / 0.95 ( 30) link_NAG-ASN : bond 0.00239 / 0.12 ( 6) link_NAG-ASN : angle 1.54233 / 1.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9438 (tp) cc_final: 0.9154 (tp) REVERT: A 95 ASP cc_start: 0.8772 (t70) cc_final: 0.8537 (t70) REVERT: A 133 GLU cc_start: 0.9413 (pm20) cc_final: 0.8862 (pm20) REVERT: A 139 VAL cc_start: 0.9774 (t) cc_final: 0.9550 (t) REVERT: A 180 MET cc_start: 0.8886 (mmm) cc_final: 0.8198 (tpp) REVERT: A 202 TYR cc_start: 0.8935 (m-80) cc_final: 0.8247 (m-80) REVERT: A 348 ASP cc_start: 0.8660 (p0) cc_final: 0.8331 (p0) REVERT: A 372 MET cc_start: 0.8934 (mmp) cc_final: 0.8566 (mmm) REVERT: A 426 TRP cc_start: 0.7684 (m100) cc_final: 0.7123 (m-10) REVERT: A 440 LYS cc_start: 0.9576 (mtmm) cc_final: 0.9212 (mtmm) REVERT: A 446 PHE cc_start: 0.8859 (m-10) cc_final: 0.8624 (m-80) REVERT: B 20 TRP cc_start: 0.8562 (p90) cc_final: 0.8233 (p90) REVERT: B 137 TYR cc_start: 0.8975 (m-80) cc_final: 0.8645 (m-10) REVERT: B 246 HIS cc_start: 0.8652 (t-170) cc_final: 0.8104 (t70) REVERT: B 287 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8669 (ttmm) REVERT: B 294 LYS cc_start: 0.9749 (mmpt) cc_final: 0.9299 (mmmt) REVERT: B 350 THR cc_start: 0.8913 (p) cc_final: 0.8654 (p) REVERT: B 383 TYR cc_start: 0.8691 (m-80) cc_final: 0.8385 (m-10) REVERT: B 396 HIS cc_start: 0.8959 (t-170) cc_final: 0.8730 (t-170) REVERT: B 423 ASP cc_start: 0.9338 (p0) cc_final: 0.9082 (p0) REVERT: B 426 TRP cc_start: 0.8284 (m100) cc_final: 0.7707 (m-10) REVERT: B 462 GLN cc_start: 0.9466 (mp10) cc_final: 0.9223 (mp-120) REVERT: B 492 LEU cc_start: 0.9700 (mt) cc_final: 0.9458 (mt) REVERT: C 20 TRP cc_start: 0.8814 (p90) cc_final: 0.8435 (p-90) REVERT: C 43 PHE cc_start: 0.9462 (m-80) cc_final: 0.9199 (m-80) REVERT: C 95 ASP cc_start: 0.8134 (t70) cc_final: 0.7917 (t0) REVERT: C 180 MET cc_start: 0.8982 (mmt) cc_final: 0.8660 (mpp) REVERT: C 287 LYS cc_start: 0.8765 (tppt) cc_final: 0.8436 (tppt) REVERT: C 296 LYS cc_start: 0.9316 (pttt) cc_final: 0.9029 (pttm) REVERT: C 385 VAL cc_start: 0.9514 (p) cc_final: 0.9303 (p) REVERT: C 418 LEU cc_start: 0.9439 (mm) cc_final: 0.9187 (mm) REVERT: C 426 TRP cc_start: 0.8542 (m100) cc_final: 0.7646 (m-10) REVERT: C 494 PHE cc_start: 0.9388 (t80) cc_final: 0.9075 (t80) REVERT: D 48 ASP cc_start: 0.8554 (p0) cc_final: 0.7622 (m-30) REVERT: D 120 TYR cc_start: 0.8571 (m-10) cc_final: 0.8205 (m-80) REVERT: D 123 LYS cc_start: 0.9738 (ttmm) cc_final: 0.9504 (mtmm) REVERT: D 126 ASN cc_start: 0.9318 (m110) cc_final: 0.9035 (m110) REVERT: E 40 ASP cc_start: 0.9250 (m-30) cc_final: 0.8813 (m-30) REVERT: E 78 TYR cc_start: 0.9431 (p90) cc_final: 0.8978 (p90) REVERT: E 83 ARG cc_start: 0.8352 (ppt170) cc_final: 0.7993 (ppt170) REVERT: E 127 TRP cc_start: 0.9245 (t60) cc_final: 0.9022 (t60) REVERT: E 158 MET cc_start: 0.9072 (mmp) cc_final: 0.8696 (ptt) REVERT: E 160 MET cc_start: 0.9158 (ttm) cc_final: 0.8938 (ttm) REVERT: F 78 TYR cc_start: 0.8599 (p90) cc_final: 0.8231 (p90) REVERT: F 89 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8369 (mtm110) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1255 time to fit residues: 78.7330 Evaluate side-chains 373 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 162 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059991 restraints weight = 72856.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061784 restraints weight = 43479.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.063021 restraints weight = 30698.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063888 restraints weight = 23969.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064472 restraints weight = 20098.947| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15635 Z= 0.199 Angle : 0.754 12.536 21289 Z= 0.386 Chirality : 0.049 0.273 2510 Planarity : 0.006 0.152 2652 Dihedral : 8.709 102.823 2542 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.46 (0.19), residues: 1950 helix: 0.82 (0.23), residues: 501 sheet: -0.05 (0.23), residues: 516 loop : -1.04 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 451 TYR 0.029 0.002 TYR B 137 PHE 0.034 0.002 PHE C 379 TRP 0.032 0.002 TRP F 143 HIS 0.006 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (15589) covalent geometry : angle 0.74285 / 0.38 (21175) SS BOND : bond 0.00586 / 0.31 ( 24) SS BOND : angle 2.02676 / 1.17 ( 48) hydrogen bonds : bond 0.03695 / 2.41 ( 658) hydrogen bonds : angle 5.45167 / 3.77 ( 1932) link_ALPHA1-3 : bond 0.00708 / 0.34 ( 3) link_ALPHA1-3 : angle 2.93508 / 1.78 ( 9) link_ALPHA1-6 : bond 0.01174 / 0.57 ( 3) link_ALPHA1-6 : angle 1.93684 / 1.24 ( 9) link_BETA1-4 : bond 0.00519 / 0.23 ( 10) link_BETA1-4 : angle 1.48180 / 0.96 ( 30) link_NAG-ASN : bond 0.00298 / 0.16 ( 6) link_NAG-ASN : angle 1.58041 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9446 (tp) cc_final: 0.9168 (tp) REVERT: A 95 ASP cc_start: 0.8763 (t70) cc_final: 0.8541 (t70) REVERT: A 133 GLU cc_start: 0.9403 (pm20) cc_final: 0.8802 (pm20) REVERT: A 139 VAL cc_start: 0.9757 (t) cc_final: 0.9450 (t) REVERT: A 180 MET cc_start: 0.8892 (mmm) cc_final: 0.8196 (tpp) REVERT: A 202 TYR cc_start: 0.8931 (m-80) cc_final: 0.8270 (m-80) REVERT: A 287 LYS cc_start: 0.8595 (pttm) cc_final: 0.8219 (ptmt) REVERT: A 348 ASP cc_start: 0.8658 (p0) cc_final: 0.8313 (p0) REVERT: A 372 MET cc_start: 0.8940 (mmp) cc_final: 0.8587 (mmm) REVERT: A 426 TRP cc_start: 0.7540 (m100) cc_final: 0.6897 (m-10) REVERT: A 446 PHE cc_start: 0.8865 (m-10) cc_final: 0.8558 (m-80) REVERT: B 20 TRP cc_start: 0.8553 (p90) cc_final: 0.8230 (p90) REVERT: B 38 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9223 (mmmm) REVERT: B 95 ASP cc_start: 0.9005 (t0) cc_final: 0.8725 (t0) REVERT: B 137 TYR cc_start: 0.8942 (m-80) cc_final: 0.8606 (m-10) REVERT: B 246 HIS cc_start: 0.8635 (t-170) cc_final: 0.8109 (t70) REVERT: B 287 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8688 (ttmm) REVERT: B 294 LYS cc_start: 0.9697 (mmpt) cc_final: 0.9308 (mmmt) REVERT: B 350 THR cc_start: 0.8885 (p) cc_final: 0.8629 (p) REVERT: B 383 TYR cc_start: 0.8679 (m-80) cc_final: 0.8361 (m-10) REVERT: B 396 HIS cc_start: 0.8924 (t-170) cc_final: 0.8691 (t-170) REVERT: B 426 TRP cc_start: 0.8341 (m100) cc_final: 0.7782 (m-10) REVERT: B 462 GLN cc_start: 0.9475 (mp10) cc_final: 0.9205 (mp10) REVERT: B 492 LEU cc_start: 0.9706 (mt) cc_final: 0.9454 (mt) REVERT: C 20 TRP cc_start: 0.8861 (p90) cc_final: 0.8527 (p-90) REVERT: C 43 PHE cc_start: 0.9436 (m-80) cc_final: 0.9198 (m-80) REVERT: C 95 ASP cc_start: 0.8115 (t70) cc_final: 0.7888 (t0) REVERT: C 155 TYR cc_start: 0.8514 (t80) cc_final: 0.7828 (t80) REVERT: C 162 ASN cc_start: 0.8802 (t160) cc_final: 0.7529 (p0) REVERT: C 180 MET cc_start: 0.8987 (mmt) cc_final: 0.8493 (mpp) REVERT: C 296 LYS cc_start: 0.9341 (pttt) cc_final: 0.9041 (pttm) REVERT: C 385 VAL cc_start: 0.9495 (p) cc_final: 0.9268 (p) REVERT: C 494 PHE cc_start: 0.9453 (t80) cc_final: 0.9127 (t80) REVERT: D 48 ASP cc_start: 0.8568 (p0) cc_final: 0.8358 (p0) REVERT: D 120 TYR cc_start: 0.8540 (m-10) cc_final: 0.8168 (m-80) REVERT: D 123 LYS cc_start: 0.9739 (ttmm) cc_final: 0.9503 (mtmm) REVERT: D 126 ASN cc_start: 0.9321 (m110) cc_final: 0.9029 (m110) REVERT: E 40 ASP cc_start: 0.9251 (m-30) cc_final: 0.8814 (m-30) REVERT: E 78 TYR cc_start: 0.9449 (p90) cc_final: 0.8987 (p90) REVERT: E 158 MET cc_start: 0.9021 (mmp) cc_final: 0.8666 (ptt) REVERT: E 160 MET cc_start: 0.9145 (ttm) cc_final: 0.8925 (ttm) REVERT: F 78 TYR cc_start: 0.8597 (p90) cc_final: 0.8228 (p90) REVERT: F 89 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8362 (mtm110) REVERT: F 130 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8145 (mmm-85) REVERT: F 143 TRP cc_start: 0.8477 (t-100) cc_final: 0.8103 (t-100) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1241 time to fit residues: 77.0388 Evaluate side-chains 363 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 263 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 81 HIS C 162 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059398 restraints weight = 73662.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.061194 restraints weight = 43850.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.062471 restraints weight = 30746.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063352 restraints weight = 23812.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063974 restraints weight = 19834.265| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15635 Z= 0.213 Angle : 0.766 11.709 21289 Z= 0.394 Chirality : 0.049 0.271 2510 Planarity : 0.006 0.141 2652 Dihedral : 8.828 103.451 2542 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.52 (0.19), residues: 1950 helix: 0.85 (0.24), residues: 486 sheet: -0.15 (0.23), residues: 516 loop : -1.05 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 417 TYR 0.029 0.002 TYR B 137 PHE 0.033 0.002 PHE F 155 TRP 0.026 0.002 TRP A 20 HIS 0.013 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (15589) covalent geometry : angle 0.75446 / 0.39 (21175) SS BOND : bond 0.00592 / 0.36 ( 24) SS BOND : angle 2.05345 / 1.22 ( 48) hydrogen bonds : bond 0.03775 / 2.47 ( 658) hydrogen bonds : angle 5.54339 / 3.83 ( 1932) link_ALPHA1-3 : bond 0.00671 / 0.32 ( 3) link_ALPHA1-3 : angle 2.93349 / 1.78 ( 9) link_ALPHA1-6 : bond 0.01229 / 0.59 ( 3) link_ALPHA1-6 : angle 1.92222 / 1.23 ( 9) link_BETA1-4 : bond 0.00517 / 0.23 ( 10) link_BETA1-4 : angle 1.48257 / 0.96 ( 30) link_NAG-ASN : bond 0.00311 / 0.16 ( 6) link_NAG-ASN : angle 1.60925 / 1.07 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9424 (tp) cc_final: 0.9138 (tp) REVERT: A 95 ASP cc_start: 0.8767 (t70) cc_final: 0.8539 (t70) REVERT: A 133 GLU cc_start: 0.9398 (pm20) cc_final: 0.8792 (pm20) REVERT: A 139 VAL cc_start: 0.9682 (t) cc_final: 0.9436 (m) REVERT: A 180 MET cc_start: 0.8754 (mmm) cc_final: 0.8235 (mmt) REVERT: A 202 TYR cc_start: 0.8912 (m-80) cc_final: 0.8269 (m-80) REVERT: A 287 LYS cc_start: 0.8594 (pttm) cc_final: 0.8198 (ptmt) REVERT: A 348 ASP cc_start: 0.8594 (p0) cc_final: 0.8240 (p0) REVERT: A 372 MET cc_start: 0.8979 (mmp) cc_final: 0.8636 (mmm) REVERT: A 426 TRP cc_start: 0.7549 (m100) cc_final: 0.6973 (m-10) REVERT: A 446 PHE cc_start: 0.8858 (m-10) cc_final: 0.8512 (m-80) REVERT: B 20 TRP cc_start: 0.8528 (p90) cc_final: 0.8229 (p90) REVERT: B 133 GLU cc_start: 0.9157 (pm20) cc_final: 0.8772 (pm20) REVERT: B 137 TYR cc_start: 0.8973 (m-80) cc_final: 0.8619 (m-10) REVERT: B 246 HIS cc_start: 0.8610 (t-170) cc_final: 0.8070 (t-90) REVERT: B 294 LYS cc_start: 0.9750 (mmpt) cc_final: 0.9338 (mmmt) REVERT: B 304 MET cc_start: 0.8868 (mmp) cc_final: 0.8475 (tpp) REVERT: B 350 THR cc_start: 0.8733 (p) cc_final: 0.8431 (p) REVERT: B 383 TYR cc_start: 0.8727 (m-80) cc_final: 0.8343 (m-10) REVERT: B 396 HIS cc_start: 0.8925 (t-170) cc_final: 0.8697 (t-170) REVERT: B 426 TRP cc_start: 0.8320 (m100) cc_final: 0.7825 (m-10) REVERT: B 492 LEU cc_start: 0.9709 (mt) cc_final: 0.9466 (mt) REVERT: C 43 PHE cc_start: 0.9375 (m-80) cc_final: 0.9144 (m-80) REVERT: C 95 ASP cc_start: 0.8027 (t70) cc_final: 0.7801 (t0) REVERT: C 155 TYR cc_start: 0.8522 (t80) cc_final: 0.7813 (t80) REVERT: C 162 ASN cc_start: 0.8790 (t160) cc_final: 0.7507 (p0) REVERT: C 180 MET cc_start: 0.8993 (mmt) cc_final: 0.8456 (mpp) REVERT: C 287 LYS cc_start: 0.8719 (tppt) cc_final: 0.8504 (tppt) REVERT: C 296 LYS cc_start: 0.9338 (pttt) cc_final: 0.9035 (pttm) REVERT: C 385 VAL cc_start: 0.9422 (p) cc_final: 0.9197 (p) REVERT: C 494 PHE cc_start: 0.9378 (t80) cc_final: 0.9076 (t80) REVERT: D 120 TYR cc_start: 0.8490 (m-10) cc_final: 0.8139 (m-80) REVERT: D 123 LYS cc_start: 0.9740 (ttmm) cc_final: 0.9503 (mtmm) REVERT: D 126 ASN cc_start: 0.9326 (m110) cc_final: 0.9038 (m110) REVERT: E 78 TYR cc_start: 0.9463 (p90) cc_final: 0.8997 (p90) REVERT: E 92 ARG cc_start: 0.7714 (tpm170) cc_final: 0.7467 (tpm170) REVERT: E 158 MET cc_start: 0.9021 (mmp) cc_final: 0.8660 (ptt) REVERT: E 160 MET cc_start: 0.9170 (ttm) cc_final: 0.8941 (ttm) REVERT: F 78 TYR cc_start: 0.8585 (p90) cc_final: 0.8242 (p90) REVERT: F 88 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7325 (tpt-90) REVERT: F 89 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8468 (mtm110) REVERT: F 130 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8110 (mmm-85) REVERT: F 143 TRP cc_start: 0.8481 (t-100) cc_final: 0.8096 (t-100) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.1202 time to fit residues: 73.3690 Evaluate side-chains 369 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 184 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 250 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN D 7 GLN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.057373 restraints weight = 75699.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059191 restraints weight = 44357.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060449 restraints weight = 30639.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.061321 restraints weight = 23638.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061939 restraints weight = 19645.438| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15635 Z= 0.272 Angle : 0.817 10.707 21289 Z= 0.422 Chirality : 0.050 0.273 2510 Planarity : 0.006 0.164 2652 Dihedral : 9.078 103.832 2542 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.12 % Allowed : 0.98 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.19), residues: 1950 helix: 0.60 (0.24), residues: 489 sheet: -0.25 (0.24), residues: 489 loop : -1.20 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 451 TYR 0.029 0.002 TYR B 137 PHE 0.039 0.003 PHE C 379 TRP 0.039 0.002 TRP A 20 HIS 0.008 0.002 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (15589) covalent geometry : angle 0.80552 / 0.42 (21175) SS BOND : bond 0.00463 / 0.25 ( 24) SS BOND : angle 2.15404 / 1.30 ( 48) hydrogen bonds : bond 0.04121 / 2.73 ( 658) hydrogen bonds : angle 5.76937 / 3.99 ( 1932) link_ALPHA1-3 : bond 0.00556 / 0.27 ( 3) link_ALPHA1-3 : angle 2.98982 / 1.79 ( 9) link_ALPHA1-6 : bond 0.01145 / 0.55 ( 3) link_ALPHA1-6 : angle 1.82888 / 1.17 ( 9) link_BETA1-4 : bond 0.00522 / 0.23 ( 10) link_BETA1-4 : angle 1.51540 / 0.97 ( 30) link_NAG-ASN : bond 0.00431 / 0.22 ( 6) link_NAG-ASN : angle 1.69873 / 1.13 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2643.92 seconds wall clock time: 46 minutes 39.87 seconds (2799.87 seconds total)