Starting phenix.real_space_refine on Tue Sep 15 00:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863.map" model { file = "/net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yeu_72863/09_2026/9yeu_72863_trim.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 10791 2.51 5 N 2675 2.21 5 O 3064 1.98 5 H 16389 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32995 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6393 Classifications: {'peptide': 397} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 6324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6324 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 6559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6559 Classifications: {'peptide': 404} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 378} Chain breaks: 3 Chain: "D" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 7006 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 6427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6427 Classifications: {'peptide': 407} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 384} Chain breaks: 1 Chain: "F" 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: "G" 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: "H" 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.54, per 1000 atoms: 0.17 Number of scatterers: 32995 At special positions: 0 Unit cell: (100.045, 107.525, 164.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 3064 8.00 N 2675 7.00 C 10791 6.00 H 16389 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.07 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.06 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.05 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN C 141 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN B 141 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 782.9 milliseconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 19 sheets defined 44.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.190A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.675A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.953A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 241 through 262 removed outlier: 3.602A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.995A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 324' Processing helix chain 'A' and resid 370 through 437 removed outlier: 3.661A pdb=" N GLY A 412 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.051A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 241 through 263 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 319 through 324 removed outlier: 4.106A pdb=" N ILE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET C 324 " --> pdb=" O ILE C 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 319 through 324' Processing helix chain 'C' and resid 370 through 436 removed outlier: 4.544A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.016A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 3.673A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.838A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 470 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.918A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.703A pdb=" N VAL D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.777A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 473 Proline residue: D 458 - end of helix removed outlier: 3.588A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.213A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.974A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 251 through 272 Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.601A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 460 removed outlier: 4.204A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.110A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.110A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 49 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.370A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.082A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.082A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.211A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 196 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR C 190 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.244A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.244A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.274A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.801A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.005A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.005A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR D 51 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 45 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR D 53 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 57 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU D 39 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU D 59 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU D 37 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY D 61 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU D 35 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N THR D 63 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 33 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 11.827A pdb=" N ASN D 65 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 14.261A pdb=" N VAL D 31 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.506A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.506A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=AB8, first strand: chain 'B' and resid 79 through 81 removed outlier: 6.904A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.221A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.221A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2778 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: 7.80 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16370 1.04 - 1.23: 359 1.23 - 1.43: 6747 1.43 - 1.63: 9815 1.63 - 1.82: 121 Bond restraints: 33412 Sorted by residual: bond pdb=" C CYS D 144 " pdb=" O CYS D 144 " ideal model delta sigma weight residual 1.234 1.183 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" NZ LYS D 224 " pdb=" HZ1 LYS D 224 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 167 " pdb=" HZ2 LYS B 167 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 66 " pdb=" HZ1 LYS A 66 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 252 " pdb=" HZ1 LYS B 252 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.59: 60458 11.59 - 23.17: 1 23.17 - 34.76: 1 34.76 - 46.34: 1 46.34 - 57.93: 2 Bond angle restraints: 60463 Sorted by residual: angle pdb=" CA PHE D 411 " pdb=" N PHE D 411 " pdb=" H PHE D 411 " ideal model delta sigma weight residual 114.00 171.93 -57.93 3.00e+00 1.11e-01 3.73e+02 angle pdb=" CA PHE A 326 " pdb=" N PHE A 326 " pdb=" H PHE A 326 " ideal model delta sigma weight residual 114.00 163.57 -49.57 3.00e+00 1.11e-01 2.73e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 156.82 -42.82 3.00e+00 1.11e-01 2.04e+02 angle pdb=" CA ARG B 401 " pdb=" N ARG B 401 " pdb=" H ARG B 401 " ideal model delta sigma weight residual 114.00 142.22 -28.22 3.00e+00 1.11e-01 8.85e+01 angle pdb=" CA HIS C 369 " pdb=" N HIS C 369 " pdb=" H HIS C 369 " ideal model delta sigma weight residual 114.00 133.43 -19.43 3.00e+00 1.11e-01 4.19e+01 ... (remaining 60458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 14855 21.13 - 42.26: 847 42.26 - 63.39: 274 63.39 - 84.52: 58 84.52 - 105.65: 26 Dihedral angle restraints: 16060 sinusoidal: 8858 harmonic: 7202 Sorted by residual: dihedral pdb=" CD ARG D 9 " pdb=" NE ARG D 9 " pdb=" CZ ARG D 9 " pdb=" NH1 ARG D 9 " ideal model delta sinusoidal sigma weight residual 0.00 77.10 -77.10 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" C ILE E 106 " pdb=" N ILE E 106 " pdb=" CA ILE E 106 " pdb=" CB ILE E 106 " ideal model delta harmonic sigma weight residual -122.00 -131.97 9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.94 105.65 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 16057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2505 0.080 - 0.160: 240 0.160 - 0.241: 6 0.241 - 0.321: 5 0.321 - 0.401: 1 Chirality restraints: 2757 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.68e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.78e+01 chirality pdb=" C1 MAN G 5 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.66e+01 ... (remaining 2754 not shown) Planarity restraints: 4782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 13 " -0.251 2.00e-02 2.50e+03 3.23e-01 1.56e+03 pdb=" CD GLN D 13 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN D 13 " 0.244 2.00e-02 2.50e+03 pdb=" NE2 GLN D 13 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN D 13 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN D 13 " -0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 9 " 0.784 9.50e-02 1.11e+02 3.35e-01 1.06e+03 pdb=" NE ARG D 9 " -0.255 2.00e-02 2.50e+03 pdb=" CZ ARG D 9 " -0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG D 9 " 0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG D 9 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG D 9 " 0.056 2.00e-02 2.50e+03 pdb="HH12 ARG D 9 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG D 9 " -0.361 2.00e-02 2.50e+03 pdb="HH22 ARG D 9 " 0.422 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.222 2.00e-02 2.50e+03 1.86e-01 4.32e+02 pdb=" C7 NAG B 501 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.008 2.00e-02 2.50e+03 ... (remaining 4779 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.80: 38 1.80 - 2.50: 23564 2.50 - 3.20: 102434 3.20 - 3.90: 138126 3.90 - 4.60: 215960 Nonbonded interactions: 480122 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 145 " pdb=" HH TYR C 190 " model vdw 1.106 2.100 nonbonded pdb=" HZ1 LYS A 145 " pdb=" HH TYR A 190 " model vdw 1.366 2.100 nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.394 2.100 nonbonded pdb=" HH TYR A 15 " pdb=" H TRP A 86 " model vdw 1.493 2.100 nonbonded pdb=" HG SER D 105 " pdb=" H ILE D 125 " model vdw 1.577 2.100 ... (remaining 480117 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' and (resid 1 through 324 or resid 369 through 436 or resid 501)) selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 17050 Z= 0.232 Angle : 0.741 19.742 23298 Z= 0.369 Chirality : 0.048 0.401 2757 Planarity : 0.011 0.478 2875 Dihedral : 16.980 105.655 6482 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 0.05 % Allowed : 9.98 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.08 (0.19), residues: 2004 helix: 2.23 (0.18), residues: 793 sheet: -0.65 (0.25), residues: 386 loop : 0.01 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.009 0.001 TYR B 67 PHE 0.020 0.001 PHE A 284 TRP 0.010 0.001 TRP A 311 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (17023) covalent geometry : angle 0.68739 / 0.36 (23223) SS BOND : bond 0.02503 / 1.29 ( 6) SS BOND : angle 3.49942 / 2.03 ( 12) hydrogen bonds : bond 0.15138 / 10.34 ( 874) hydrogen bonds : angle 6.27991 / 4.49 ( 2778) link_ALPHA1-3 : bond 0.00191 / 0.09 ( 2) link_ALPHA1-3 : angle 2.17894 / 1.07 ( 6) link_ALPHA1-6 : bond 0.00260 / 0.13 ( 3) link_ALPHA1-6 : angle 0.95825 / 0.51 ( 9) link_BETA1-4 : bond 0.01043 / 0.71 ( 10) link_BETA1-4 : angle 3.34321 / 2.29 ( 30) link_NAG-ASN : bond 0.11970 / 6.53 ( 6) link_NAG-ASN : angle 8.49512 / 4.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.7450 (mtmt) cc_final: 0.7201 (mttp) REVERT: A 279 LEU cc_start: 0.8305 (tp) cc_final: 0.8039 (mp) REVERT: C 280 PHE cc_start: 0.7480 (m-10) cc_final: 0.6548 (t80) REVERT: C 376 ILE cc_start: 0.7889 (mt) cc_final: 0.7676 (tt) REVERT: C 384 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6769 (mt-10) REVERT: C 387 LYS cc_start: 0.7894 (tptm) cc_final: 0.7669 (tptm) REVERT: C 391 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7340 (mm-30) REVERT: C 401 TYR cc_start: 0.8403 (t80) cc_final: 0.8123 (t80) REVERT: E 6 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7700 (mtm-85) REVERT: E 330 LYS cc_start: 0.7666 (mttt) cc_final: 0.7354 (mmtm) REVERT: E 333 LEU cc_start: 0.8469 (mt) cc_final: 0.8221 (mm) REVERT: E 422 ARG cc_start: 0.7465 (ttp-110) cc_final: 0.7201 (mtp180) REVERT: D 167 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7784 (tptp) REVERT: D 332 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6788 (mm-30) REVERT: D 451 LEU cc_start: 0.8670 (tp) cc_final: 0.8466 (tm) REVERT: B 268 PHE cc_start: 0.7593 (t80) cc_final: 0.7084 (m-10) REVERT: B 286 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7208 (mtp180) REVERT: B 430 MET cc_start: 0.7805 (mtm) cc_final: 0.7574 (ttm) outliers start: 1 outliers final: 2 residues processed: 325 average time/residue: 1.0856 time to fit residues: 400.3172 Evaluate side-chains 229 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain B residue 274 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS C 27 GLN C 306 HIS E 208 GLN D 60 HIS B 14 ASN B 99 GLN B 272 GLN B 310 GLN B 316 HIS B 432 ASN B 472 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108946 restraints weight = 56713.925| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.90 r_work: 0.3221 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17050 Z= 0.142 Angle : 0.553 5.929 23298 Z= 0.278 Chirality : 0.044 0.169 2757 Planarity : 0.006 0.229 2875 Dihedral : 9.692 83.238 2607 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 1.08 % Allowed : 13.22 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.49 (0.19), residues: 2004 helix: 2.72 (0.18), residues: 796 sheet: -0.47 (0.25), residues: 388 loop : 0.07 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 9 TYR 0.012 0.001 TYR D 119 PHE 0.015 0.001 PHE A 284 TRP 0.008 0.001 TRP E 322 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (17023) covalent geometry : angle 0.53905 / 0.28 (23223) SS BOND : bond 0.00436 / 0.23 ( 6) SS BOND : angle 1.60216 / 0.95 ( 12) hydrogen bonds : bond 0.04869 / 3.31 ( 874) hydrogen bonds : angle 4.65957 / 3.28 ( 2778) link_ALPHA1-3 : bond 0.00540 / 0.26 ( 2) link_ALPHA1-3 : angle 1.88978 / 1.04 ( 6) link_ALPHA1-6 : bond 0.00523 / 0.26 ( 3) link_ALPHA1-6 : angle 1.92727 / 1.13 ( 9) link_BETA1-4 : bond 0.00370 / 0.25 ( 10) link_BETA1-4 : angle 2.57069 / 1.80 ( 30) link_NAG-ASN : bond 0.00590 / 0.44 ( 6) link_NAG-ASN : angle 2.38263 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8833 (t0) cc_final: 0.8610 (t0) REVERT: A 276 LYS cc_start: 0.7269 (mtmt) cc_final: 0.7009 (mtmt) REVERT: A 279 LEU cc_start: 0.8150 (tp) cc_final: 0.7839 (mp) REVERT: C 280 PHE cc_start: 0.7329 (m-10) cc_final: 0.6070 (t80) REVERT: C 282 MET cc_start: 0.8107 (mtp) cc_final: 0.7750 (mtp) REVERT: C 391 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7255 (mm-30) REVERT: C 401 TYR cc_start: 0.8393 (t80) cc_final: 0.8073 (t80) REVERT: E 6 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7632 (mtm-85) REVERT: E 330 LYS cc_start: 0.7577 (mttt) cc_final: 0.7231 (mmtm) REVERT: E 333 LEU cc_start: 0.8372 (mt) cc_final: 0.8154 (mm) REVERT: E 422 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.7104 (mtp180) REVERT: D 5 GLU cc_start: 0.7903 (tt0) cc_final: 0.7612 (tt0) REVERT: D 167 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7420 (tptp) REVERT: D 332 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6824 (mm-30) REVERT: D 436 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 451 LEU cc_start: 0.8517 (tp) cc_final: 0.8209 (tm) REVERT: B 268 PHE cc_start: 0.7527 (t80) cc_final: 0.6713 (m-10) REVERT: B 286 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6934 (mtp180) outliers start: 20 outliers final: 9 residues processed: 240 average time/residue: 1.0567 time to fit residues: 290.8591 Evaluate side-chains 220 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 274 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 147 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 208 GLN E 208 GLN B 14 ASN B 99 GLN B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106406 restraints weight = 57561.312| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.75 r_work: 0.3178 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17050 Z= 0.190 Angle : 0.563 5.600 23298 Z= 0.284 Chirality : 0.045 0.198 2757 Planarity : 0.005 0.043 2875 Dihedral : 8.209 75.874 2607 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 1.57 % Allowed : 12.68 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.43 (0.19), residues: 2004 helix: 2.67 (0.17), residues: 795 sheet: -0.42 (0.25), residues: 399 loop : -0.00 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 9 TYR 0.012 0.002 TYR A 72 PHE 0.015 0.002 PHE D 291 TRP 0.010 0.001 TRP D 176 HIS 0.010 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (17023) covalent geometry : angle 0.54936 / 0.28 (23223) SS BOND : bond 0.00466 / 0.25 ( 6) SS BOND : angle 1.75305 / 1.04 ( 12) hydrogen bonds : bond 0.04623 / 3.14 ( 874) hydrogen bonds : angle 4.44636 / 3.11 ( 2778) link_ALPHA1-3 : bond 0.00716 / 0.34 ( 2) link_ALPHA1-3 : angle 1.43620 / 0.83 ( 6) link_ALPHA1-6 : bond 0.00604 / 0.30 ( 3) link_ALPHA1-6 : angle 1.67184 / 0.97 ( 9) link_BETA1-4 : bond 0.00513 / 0.33 ( 10) link_BETA1-4 : angle 2.75421 / 1.94 ( 30) link_NAG-ASN : bond 0.00259 / 0.13 ( 6) link_NAG-ASN : angle 2.11932 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8050 (mtm110) REVERT: A 276 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7070 (mtmt) REVERT: A 326 PHE cc_start: 0.5779 (m-80) cc_final: 0.5565 (m-80) REVERT: A 407 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: C 273 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7655 (mm) REVERT: C 280 PHE cc_start: 0.7332 (m-10) cc_final: 0.6073 (t80) REVERT: C 282 MET cc_start: 0.8075 (mtp) cc_final: 0.7768 (mtp) REVERT: C 310 ASN cc_start: 0.7583 (t0) cc_final: 0.7220 (t0) REVERT: C 391 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7236 (mm-30) REVERT: C 401 TYR cc_start: 0.8473 (t80) cc_final: 0.8206 (t80) REVERT: C 407 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6285 (m-30) REVERT: E 330 LYS cc_start: 0.7709 (mttt) cc_final: 0.7307 (mmtm) REVERT: E 333 LEU cc_start: 0.8373 (mt) cc_final: 0.8164 (mm) REVERT: E 422 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7042 (mtp180) REVERT: E 427 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7334 (mm-40) REVERT: D 167 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7451 (tptp) REVERT: D 332 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6793 (mm-30) REVERT: D 436 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: D 451 LEU cc_start: 0.8421 (tp) cc_final: 0.8102 (tm) REVERT: B 268 PHE cc_start: 0.7458 (t80) cc_final: 0.6684 (m-10) REVERT: B 286 ARG cc_start: 0.7705 (mtt180) cc_final: 0.6975 (mtp180) REVERT: B 416 ASP cc_start: 0.7254 (m-30) cc_final: 0.7044 (m-30) outliers start: 29 outliers final: 10 residues processed: 241 average time/residue: 1.0401 time to fit residues: 287.7008 Evaluate side-chains 228 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 155 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 208 GLN E 315 HIS B 14 ASN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106839 restraints weight = 57497.505| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.75 r_work: 0.3185 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17050 Z= 0.160 Angle : 0.533 5.243 23298 Z= 0.268 Chirality : 0.044 0.193 2757 Planarity : 0.004 0.042 2875 Dihedral : 7.470 68.425 2605 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 1.30 % Allowed : 13.38 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.47 (0.19), residues: 2004 helix: 2.75 (0.17), residues: 795 sheet: -0.43 (0.25), residues: 414 loop : -0.02 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 9 TYR 0.010 0.001 TYR D 119 PHE 0.012 0.001 PHE B 439 TRP 0.008 0.001 TRP D 176 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (17023) covalent geometry : angle 0.52118 / 0.27 (23223) SS BOND : bond 0.00360 / 0.18 ( 6) SS BOND : angle 1.46315 / 0.86 ( 12) hydrogen bonds : bond 0.04312 / 2.93 ( 874) hydrogen bonds : angle 4.30639 / 3.01 ( 2778) link_ALPHA1-3 : bond 0.00851 / 0.41 ( 2) link_ALPHA1-3 : angle 1.77637 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00644 / 0.31 ( 3) link_ALPHA1-6 : angle 1.73744 / 0.98 ( 9) link_BETA1-4 : bond 0.00379 / 0.24 ( 10) link_BETA1-4 : angle 2.41372 / 1.70 ( 30) link_NAG-ASN : bond 0.00075 / 0.05 ( 6) link_NAG-ASN : angle 1.99566 / 1.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7984 (mtm110) REVERT: A 276 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6953 (mtmt) REVERT: A 326 PHE cc_start: 0.5878 (m-80) cc_final: 0.5530 (m-80) REVERT: A 387 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7653 (tptm) REVERT: C 280 PHE cc_start: 0.7323 (m-10) cc_final: 0.6056 (t80) REVERT: C 391 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7246 (mm-30) REVERT: C 401 TYR cc_start: 0.8481 (t80) cc_final: 0.8209 (t80) REVERT: C 407 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6321 (m-30) REVERT: E 330 LYS cc_start: 0.7656 (mttt) cc_final: 0.7286 (mmtm) REVERT: E 427 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: E 431 ASP cc_start: 0.7642 (m-30) cc_final: 0.7374 (m-30) REVERT: D 167 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7504 (tptp) REVERT: D 241 PHE cc_start: 0.8468 (m-10) cc_final: 0.8258 (m-10) REVERT: D 332 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6693 (mm-30) REVERT: D 436 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: D 451 LEU cc_start: 0.8396 (tp) cc_final: 0.8067 (tm) REVERT: B 225 ILE cc_start: 0.8397 (mt) cc_final: 0.7898 (pt) REVERT: B 268 PHE cc_start: 0.7440 (t80) cc_final: 0.6673 (m-10) REVERT: B 286 ARG cc_start: 0.7683 (mtt180) cc_final: 0.6964 (mtp180) outliers start: 24 outliers final: 8 residues processed: 238 average time/residue: 1.0416 time to fit residues: 284.9448 Evaluate side-chains 229 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 208 GLN B 13 ASN B 14 ASN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105896 restraints weight = 57855.948| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.76 r_work: 0.3172 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17050 Z= 0.194 Angle : 0.555 6.596 23298 Z= 0.279 Chirality : 0.044 0.191 2757 Planarity : 0.005 0.041 2875 Dihedral : 7.261 67.712 2605 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 13.28 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.41 (0.19), residues: 2004 helix: 2.71 (0.17), residues: 795 sheet: -0.42 (0.25), residues: 408 loop : -0.08 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.012 0.002 TYR A 72 PHE 0.014 0.002 PHE D 291 TRP 0.010 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (17023) covalent geometry : angle 0.54234 / 0.28 (23223) SS BOND : bond 0.00454 / 0.24 ( 6) SS BOND : angle 1.65268 / 0.96 ( 12) hydrogen bonds : bond 0.04409 / 3.00 ( 874) hydrogen bonds : angle 4.33197 / 3.03 ( 2778) link_ALPHA1-3 : bond 0.00726 / 0.35 ( 2) link_ALPHA1-3 : angle 1.49576 / 0.86 ( 6) link_ALPHA1-6 : bond 0.00773 / 0.38 ( 3) link_ALPHA1-6 : angle 1.56556 / 0.89 ( 9) link_BETA1-4 : bond 0.00447 / 0.29 ( 10) link_BETA1-4 : angle 2.55262 / 1.78 ( 30) link_NAG-ASN : bond 0.00145 / 0.07 ( 6) link_NAG-ASN : angle 2.08080 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.907 Fit side-chains REVERT: A 6 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7869 (mtm110) REVERT: A 76 LYS cc_start: 0.8444 (mttm) cc_final: 0.8235 (mttm) REVERT: A 129 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: A 276 LYS cc_start: 0.7305 (mtmt) cc_final: 0.6964 (mtmt) REVERT: A 279 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 326 PHE cc_start: 0.6052 (m-80) cc_final: 0.5693 (m-80) REVERT: A 387 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7838 (tptm) REVERT: C 280 PHE cc_start: 0.7325 (m-10) cc_final: 0.6061 (t80) REVERT: C 282 MET cc_start: 0.8035 (mtp) cc_final: 0.7718 (mtp) REVERT: C 391 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7274 (mm-30) REVERT: C 401 TYR cc_start: 0.8494 (t80) cc_final: 0.8227 (t80) REVERT: C 407 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6313 (m-30) REVERT: E 330 LYS cc_start: 0.7701 (mttt) cc_final: 0.7318 (mmtm) REVERT: E 427 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7348 (mm-40) REVERT: E 431 ASP cc_start: 0.7645 (m-30) cc_final: 0.7372 (m-30) REVERT: D 167 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7509 (tptp) REVERT: D 241 PHE cc_start: 0.8482 (m-10) cc_final: 0.8279 (m-10) REVERT: D 332 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6726 (mm-30) REVERT: D 436 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: D 451 LEU cc_start: 0.8403 (tp) cc_final: 0.8084 (tm) REVERT: B 23 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7605 (mtt180) REVERT: B 225 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7915 (pt) REVERT: B 268 PHE cc_start: 0.7443 (t80) cc_final: 0.6673 (m-10) REVERT: B 286 ARG cc_start: 0.7671 (mtt180) cc_final: 0.6934 (mtp180) outliers start: 33 outliers final: 13 residues processed: 243 average time/residue: 1.0943 time to fit residues: 303.1412 Evaluate side-chains 239 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 83 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 13 ASN B 99 GLN B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106389 restraints weight = 58070.341| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.76 r_work: 0.3178 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17050 Z= 0.160 Angle : 0.533 6.059 23298 Z= 0.268 Chirality : 0.043 0.196 2757 Planarity : 0.004 0.040 2875 Dihedral : 6.793 63.718 2605 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 1.57 % Allowed : 13.55 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.47 (0.19), residues: 2004 helix: 2.77 (0.18), residues: 795 sheet: -0.44 (0.25), residues: 408 loop : -0.03 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 127 TYR 0.010 0.001 TYR D 119 PHE 0.012 0.001 PHE A 284 TRP 0.008 0.001 TRP D 176 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (17023) covalent geometry : angle 0.52106 / 0.27 (23223) SS BOND : bond 0.00386 / 0.21 ( 6) SS BOND : angle 1.44390 / 0.84 ( 12) hydrogen bonds : bond 0.04233 / 2.88 ( 874) hydrogen bonds : angle 4.24338 / 2.96 ( 2778) link_ALPHA1-3 : bond 0.00744 / 0.35 ( 2) link_ALPHA1-3 : angle 1.61673 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00943 / 0.46 ( 3) link_ALPHA1-6 : angle 1.86225 / 1.02 ( 9) link_BETA1-4 : bond 0.00380 / 0.25 ( 10) link_BETA1-4 : angle 2.32381 / 1.64 ( 30) link_NAG-ASN : bond 0.00074 / 0.05 ( 6) link_NAG-ASN : angle 1.97384 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7924 (mtm110) REVERT: A 76 LYS cc_start: 0.8437 (mttm) cc_final: 0.8231 (mttm) REVERT: A 276 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6950 (mtmt) REVERT: A 326 PHE cc_start: 0.6107 (m-80) cc_final: 0.5697 (m-80) REVERT: A 387 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (tptm) REVERT: C 280 PHE cc_start: 0.7226 (m-10) cc_final: 0.6000 (t80) REVERT: C 282 MET cc_start: 0.8061 (mtp) cc_final: 0.7747 (mtp) REVERT: C 391 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7275 (mm-30) REVERT: C 401 TYR cc_start: 0.8474 (t80) cc_final: 0.8218 (t80) REVERT: C 407 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6273 (m-30) REVERT: E 330 LYS cc_start: 0.7740 (mttt) cc_final: 0.7371 (mmtm) REVERT: E 427 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: E 431 ASP cc_start: 0.7646 (m-30) cc_final: 0.7370 (m-30) REVERT: D 167 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7446 (tptp) REVERT: D 170 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.4975 (ttp80) REVERT: D 207 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7909 (mm) REVERT: D 241 PHE cc_start: 0.8475 (m-10) cc_final: 0.8267 (m-10) REVERT: D 332 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6722 (mm-30) REVERT: D 436 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 451 LEU cc_start: 0.8391 (tp) cc_final: 0.8074 (tm) REVERT: B 225 ILE cc_start: 0.8398 (mt) cc_final: 0.7895 (pt) REVERT: B 268 PHE cc_start: 0.7440 (t80) cc_final: 0.6674 (m-10) REVERT: B 286 ARG cc_start: 0.7672 (mtt180) cc_final: 0.6936 (mtp180) outliers start: 29 outliers final: 12 residues processed: 244 average time/residue: 1.0515 time to fit residues: 293.7838 Evaluate side-chains 237 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 198 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 13 ASN B 14 ASN B 99 GLN B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104406 restraints weight = 58197.607| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17050 Z= 0.247 Angle : 0.594 6.694 23298 Z= 0.300 Chirality : 0.045 0.214 2757 Planarity : 0.005 0.044 2875 Dihedral : 7.198 66.791 2605 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 1.83 % Allowed : 13.60 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.33 (0.19), residues: 2004 helix: 2.61 (0.18), residues: 795 sheet: -0.43 (0.25), residues: 409 loop : -0.11 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 218 TYR 0.013 0.002 TYR A 72 PHE 0.016 0.002 PHE D 291 TRP 0.012 0.002 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (17023) covalent geometry : angle 0.58003 / 0.30 (23223) SS BOND : bond 0.00531 / 0.28 ( 6) SS BOND : angle 1.89908 / 1.10 ( 12) hydrogen bonds : bond 0.04621 / 3.15 ( 874) hydrogen bonds : angle 4.40377 / 3.07 ( 2778) link_ALPHA1-3 : bond 0.00655 / 0.31 ( 2) link_ALPHA1-3 : angle 1.51701 / 0.88 ( 6) link_ALPHA1-6 : bond 0.01004 / 0.49 ( 3) link_ALPHA1-6 : angle 1.64373 / 0.91 ( 9) link_BETA1-4 : bond 0.00542 / 0.34 ( 10) link_BETA1-4 : angle 2.75910 / 1.93 ( 30) link_NAG-ASN : bond 0.00256 / 0.12 ( 6) link_NAG-ASN : angle 2.16992 / 1.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8089 (mtm110) REVERT: A 129 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 276 LYS cc_start: 0.7393 (mtmt) cc_final: 0.7065 (mtmt) REVERT: A 326 PHE cc_start: 0.6130 (m-80) cc_final: 0.5694 (m-80) REVERT: A 387 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7912 (tptm) REVERT: C 280 PHE cc_start: 0.7261 (m-10) cc_final: 0.6047 (t80) REVERT: C 282 MET cc_start: 0.8149 (mtp) cc_final: 0.7941 (mtp) REVERT: C 391 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7342 (mm-30) REVERT: C 401 TYR cc_start: 0.8506 (t80) cc_final: 0.8215 (t80) REVERT: C 407 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6323 (m-30) REVERT: E 6 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7342 (mtm110) REVERT: E 330 LYS cc_start: 0.7797 (mttt) cc_final: 0.7477 (mmtp) REVERT: E 427 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7390 (mm-40) REVERT: E 431 ASP cc_start: 0.7808 (m-30) cc_final: 0.7535 (m-30) REVERT: D 167 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7537 (tptp) REVERT: D 170 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5023 (ttp80) REVERT: D 207 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7929 (mm) REVERT: D 241 PHE cc_start: 0.8511 (m-10) cc_final: 0.8304 (m-10) REVERT: D 332 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6746 (mm-30) REVERT: D 436 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: D 451 LEU cc_start: 0.8463 (tp) cc_final: 0.8150 (tm) REVERT: B 131 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: B 268 PHE cc_start: 0.7542 (t80) cc_final: 0.6761 (m-10) REVERT: B 286 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7011 (mtp180) REVERT: B 330 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5751 (tm) outliers start: 34 outliers final: 12 residues processed: 243 average time/residue: 1.1683 time to fit residues: 323.9960 Evaluate side-chains 235 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 13 ASN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105691 restraints weight = 57992.442| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.73 r_work: 0.3167 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17050 Z= 0.177 Angle : 0.554 7.671 23298 Z= 0.279 Chirality : 0.044 0.227 2757 Planarity : 0.004 0.038 2875 Dihedral : 6.906 63.635 2605 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 13.82 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.38 (0.19), residues: 2004 helix: 2.66 (0.18), residues: 795 sheet: -0.42 (0.25), residues: 408 loop : -0.09 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 127 TYR 0.010 0.001 TYR A 72 PHE 0.015 0.001 PHE A 284 TRP 0.009 0.001 TRP D 176 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (17023) covalent geometry : angle 0.54274 / 0.28 (23223) SS BOND : bond 0.00391 / 0.21 ( 6) SS BOND : angle 1.50304 / 0.87 ( 12) hydrogen bonds : bond 0.04337 / 2.95 ( 874) hydrogen bonds : angle 4.29541 / 3.00 ( 2778) link_ALPHA1-3 : bond 0.00684 / 0.33 ( 2) link_ALPHA1-3 : angle 1.56034 / 0.89 ( 6) link_ALPHA1-6 : bond 0.01033 / 0.50 ( 3) link_ALPHA1-6 : angle 1.97474 / 1.08 ( 9) link_BETA1-4 : bond 0.00395 / 0.26 ( 10) link_BETA1-4 : angle 2.39804 / 1.71 ( 30) link_NAG-ASN : bond 0.00101 / 0.06 ( 6) link_NAG-ASN : angle 1.97273 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7830 (mtm110) REVERT: A 129 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: A 276 LYS cc_start: 0.7322 (mtmt) cc_final: 0.6983 (mtmt) REVERT: A 279 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 326 PHE cc_start: 0.6123 (m-80) cc_final: 0.5656 (m-80) REVERT: A 387 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7974 (tptm) REVERT: C 280 PHE cc_start: 0.7205 (m-10) cc_final: 0.5990 (t80) REVERT: C 282 MET cc_start: 0.8074 (mtp) cc_final: 0.7838 (mtp) REVERT: C 391 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7336 (mm-30) REVERT: C 401 TYR cc_start: 0.8466 (t80) cc_final: 0.8169 (t80) REVERT: C 407 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6281 (m-30) REVERT: E 6 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7253 (mtm110) REVERT: E 321 LEU cc_start: 0.7308 (tp) cc_final: 0.7088 (tp) REVERT: E 330 LYS cc_start: 0.7754 (mttt) cc_final: 0.7427 (mmtp) REVERT: E 427 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: E 431 ASP cc_start: 0.7690 (m-30) cc_final: 0.7397 (m-30) REVERT: D 167 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7454 (tptp) REVERT: D 170 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5020 (ttp80) REVERT: D 207 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7892 (mm) REVERT: D 241 PHE cc_start: 0.8478 (m-10) cc_final: 0.8266 (m-10) REVERT: D 332 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6727 (mm-30) REVERT: D 426 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (m110) REVERT: D 436 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: D 451 LEU cc_start: 0.8398 (tp) cc_final: 0.8079 (tm) REVERT: B 268 PHE cc_start: 0.7451 (t80) cc_final: 0.6647 (m-10) REVERT: B 286 ARG cc_start: 0.7691 (mtt180) cc_final: 0.6943 (mtp180) REVERT: B 330 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5775 (tm) outliers start: 30 outliers final: 11 residues processed: 239 average time/residue: 1.1290 time to fit residues: 309.1825 Evaluate side-chains 237 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 13 ASN B 14 ASN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105800 restraints weight = 57827.861| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.73 r_work: 0.3167 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17050 Z= 0.176 Angle : 0.550 7.708 23298 Z= 0.276 Chirality : 0.044 0.240 2757 Planarity : 0.004 0.039 2875 Dihedral : 6.783 60.876 2605 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 1.57 % Allowed : 13.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.41 (0.19), residues: 2004 helix: 2.69 (0.18), residues: 795 sheet: -0.42 (0.25), residues: 407 loop : -0.07 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 324 TYR 0.011 0.001 TYR A 72 PHE 0.016 0.001 PHE E 464 TRP 0.009 0.001 TRP D 176 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (17023) covalent geometry : angle 0.53803 / 0.27 (23223) SS BOND : bond 0.00404 / 0.21 ( 6) SS BOND : angle 1.53710 / 0.89 ( 12) hydrogen bonds : bond 0.04294 / 2.92 ( 874) hydrogen bonds : angle 4.26094 / 2.97 ( 2778) link_ALPHA1-3 : bond 0.00711 / 0.34 ( 2) link_ALPHA1-3 : angle 1.55036 / 0.89 ( 6) link_ALPHA1-6 : bond 0.01101 / 0.53 ( 3) link_ALPHA1-6 : angle 1.89502 / 1.04 ( 9) link_BETA1-4 : bond 0.00402 / 0.26 ( 10) link_BETA1-4 : angle 2.41781 / 1.71 ( 30) link_NAG-ASN : bond 0.00128 / 0.07 ( 6) link_NAG-ASN : angle 2.03385 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.955 Fit side-chains REVERT: A 6 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: A 129 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: A 276 LYS cc_start: 0.7374 (mtmt) cc_final: 0.7049 (mtmt) REVERT: A 387 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8018 (tptm) REVERT: C 280 PHE cc_start: 0.7272 (m-10) cc_final: 0.6051 (t80) REVERT: C 282 MET cc_start: 0.8071 (mtp) cc_final: 0.7836 (mtp) REVERT: C 391 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7439 (mm-30) REVERT: C 401 TYR cc_start: 0.8501 (t80) cc_final: 0.8218 (t80) REVERT: C 407 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6307 (m-30) REVERT: E 6 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7303 (mtm110) REVERT: E 321 LEU cc_start: 0.7274 (tp) cc_final: 0.7051 (tp) REVERT: E 330 LYS cc_start: 0.7751 (mttt) cc_final: 0.7440 (mmtp) REVERT: E 427 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: E 431 ASP cc_start: 0.7724 (m-30) cc_final: 0.7455 (m-30) REVERT: D 167 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7479 (tptp) REVERT: D 170 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.5048 (ttp80) REVERT: D 207 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 241 PHE cc_start: 0.8508 (m-10) cc_final: 0.8297 (m-10) REVERT: D 332 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: D 436 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: D 451 LEU cc_start: 0.8452 (tp) cc_final: 0.8149 (tm) REVERT: B 268 PHE cc_start: 0.7488 (t80) cc_final: 0.6714 (m-10) REVERT: B 286 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7000 (mtp180) REVERT: B 330 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.5786 (tm) outliers start: 29 outliers final: 11 residues processed: 240 average time/residue: 1.1328 time to fit residues: 312.3032 Evaluate side-chains 232 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 149 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 13 ASN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107160 restraints weight = 58051.497| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.74 r_work: 0.3190 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17050 Z= 0.124 Angle : 0.520 9.060 23298 Z= 0.261 Chirality : 0.043 0.235 2757 Planarity : 0.004 0.039 2875 Dihedral : 6.355 58.558 2605 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 1.19 % Allowed : 14.19 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.53 (0.19), residues: 2004 helix: 2.81 (0.18), residues: 795 sheet: -0.41 (0.25), residues: 405 loop : 0.02 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 20 TYR 0.010 0.001 TYR D 434 PHE 0.016 0.001 PHE A 284 TRP 0.008 0.001 TRP C 311 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (17023) covalent geometry : angle 0.51033 / 0.26 (23223) SS BOND : bond 0.00287 / 0.15 ( 6) SS BOND : angle 1.17364 / 0.67 ( 12) hydrogen bonds : bond 0.04015 / 2.73 ( 874) hydrogen bonds : angle 4.13815 / 2.88 ( 2778) link_ALPHA1-3 : bond 0.00771 / 0.37 ( 2) link_ALPHA1-3 : angle 1.71787 / 0.96 ( 6) link_ALPHA1-6 : bond 0.01144 / 0.55 ( 3) link_ALPHA1-6 : angle 2.02830 / 1.09 ( 9) link_BETA1-4 : bond 0.00333 / 0.22 ( 10) link_BETA1-4 : angle 2.07997 / 1.49 ( 30) link_NAG-ASN : bond 0.00120 / 0.08 ( 6) link_NAG-ASN : angle 1.86317 / 1.26 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7926 (mtm110) REVERT: A 129 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: A 276 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6951 (mtmt) REVERT: A 387 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7965 (tptm) REVERT: C 280 PHE cc_start: 0.7208 (m-10) cc_final: 0.6028 (t80) REVERT: C 282 MET cc_start: 0.8000 (mtp) cc_final: 0.7695 (mtp) REVERT: C 391 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7376 (mm-30) REVERT: C 401 TYR cc_start: 0.8473 (t80) cc_final: 0.8189 (t80) REVERT: C 407 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6249 (m-30) REVERT: E 6 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7200 (mtm110) REVERT: E 321 LEU cc_start: 0.7234 (tp) cc_final: 0.6999 (tp) REVERT: E 330 LYS cc_start: 0.7709 (mttt) cc_final: 0.7385 (mmtp) REVERT: E 427 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7284 (mm-40) REVERT: E 431 ASP cc_start: 0.7691 (m-30) cc_final: 0.7395 (m-30) REVERT: D 167 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7440 (tptp) REVERT: D 170 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5178 (ttp80) REVERT: D 207 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 241 PHE cc_start: 0.8471 (m-10) cc_final: 0.8258 (m-10) REVERT: D 332 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: D 436 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: D 451 LEU cc_start: 0.8377 (tp) cc_final: 0.8070 (tm) REVERT: B 268 PHE cc_start: 0.7393 (t80) cc_final: 0.6621 (m-10) REVERT: B 286 ARG cc_start: 0.7676 (mtt180) cc_final: 0.6937 (mtp180) REVERT: B 330 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.5822 (tm) outliers start: 22 outliers final: 8 residues processed: 240 average time/residue: 1.1356 time to fit residues: 312.6545 Evaluate side-chains 234 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 127 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN E 208 GLN B 99 GLN B 301 ASN B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106822 restraints weight = 57965.584| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.73 r_work: 0.3185 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17050 Z= 0.146 Angle : 0.530 9.073 23298 Z= 0.265 Chirality : 0.043 0.248 2757 Planarity : 0.004 0.040 2875 Dihedral : 6.189 56.260 2605 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 1.35 % Allowed : 14.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % 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: 1.52 (0.19), residues: 2004 helix: 2.78 (0.18), residues: 795 sheet: -0.38 (0.25), residues: 405 loop : 0.02 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 209 TYR 0.009 0.001 TYR A 72 PHE 0.018 0.001 PHE E 464 TRP 0.008 0.001 TRP E 322 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (17023) covalent geometry : angle 0.51938 / 0.26 (23223) SS BOND : bond 0.00345 / 0.18 ( 6) SS BOND : angle 1.35550 / 0.78 ( 12) hydrogen bonds : bond 0.04073 / 2.76 ( 874) hydrogen bonds : angle 4.13797 / 2.88 ( 2778) link_ALPHA1-3 : bond 0.00772 / 0.37 ( 2) link_ALPHA1-3 : angle 1.65629 / 0.93 ( 6) link_ALPHA1-6 : bond 0.01172 / 0.56 ( 3) link_ALPHA1-6 : angle 1.87212 / 1.00 ( 9) link_BETA1-4 : bond 0.00362 / 0.23 ( 10) link_BETA1-4 : angle 2.21728 / 1.57 ( 30) link_NAG-ASN : bond 0.00087 / 0.05 ( 6) link_NAG-ASN : angle 1.95698 / 1.32 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11245.19 seconds wall clock time: 190 minutes 37.82 seconds (11437.82 seconds total)