Starting phenix.real_space_refine on Thu Mar 5 00:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sms_25207/03_2026/7sms_25207.map" } resolution = 3.18 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= 0.000 sd= 0.003 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 P 5 5.49 5 S 85 5.16 5 C 11202 2.51 5 N 2640 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17051 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'POV': 1, 'TC9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 1, 'POV': 1, 'TC9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'POV': 1, 'TC9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 CLR A 501 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 501 " occ=0.80 residue: pdb=" N POV B 603 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 603 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 502 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 502 " occ=0.75 residue: pdb=" N POV D 503 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 503 " occ=0.75 residue: pdb=" N POV E 602 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV E 602 " occ=0.75 Time building chain proxies: 3.90, per 1000 atoms: 0.23 Number of scatterers: 17051 At special positions: 0 Unit cell: (162.549, 125.12, 100.524, 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 85 16.00 P 5 15.00 O 3119 8.00 N 2640 7.00 C 11202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.07 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG 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 F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 806.9 milliseconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 20 sheets defined 43.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.697A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.715A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.586A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.726A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 263 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.739A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.517A pdb=" N ALA A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.504A pdb=" N VAL B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.676A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 417 through 476 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.073A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.965A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.679A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.502A pdb=" N GLY C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.781A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.156A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.136A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.554A pdb=" N VAL D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 324' Processing helix chain 'D' and resid 371 through 426 Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.517A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.927A pdb=" N GLU E 73 " --> pdb=" O SER 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 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.579A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.705A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 removed outlier: 3.610A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.149A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.149A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 49 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.557A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.931A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.931A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR B 51 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 45 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 59 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 37 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 35 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N TYR B 63 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 33 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N HIS B 65 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N VAL B 31 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.186A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG B 222 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 192 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.186A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.298A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.298A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.400A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.400A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.821A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.821A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.614A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.825A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.825A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.204A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS E 188 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN E 216 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE E 186 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.204A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 927 hydrogen bonds defined for protein. 2673 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: 3.09 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2633 1.31 - 1.45: 4895 1.45 - 1.58: 9844 1.58 - 1.71: 10 1.71 - 1.84: 139 Bond restraints: 17521 Sorted by residual: bond pdb=" C19 TC9 B 602 " pdb=" C24 TC9 B 602 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C19 TC9 E 601 " pdb=" C24 TC9 E 601 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C19 TC9 B 601 " pdb=" C24 TC9 B 601 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C19 TC9 D 501 " pdb=" C24 TC9 D 501 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C19 TC9 E 601 " pdb=" N20 TC9 E 601 " ideal model delta sigma weight residual 1.540 1.482 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 17516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 23446 2.49 - 4.97: 408 4.97 - 7.46: 59 7.46 - 9.95: 7 9.95 - 12.43: 10 Bond angle restraints: 23930 Sorted by residual: angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 110.10 -12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" O11 POV B 603 " pdb=" P POV B 603 " pdb=" O12 POV B 603 " ideal model delta sigma weight residual 97.67 109.37 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O13 POV B 603 " pdb=" P POV B 603 " pdb=" O14 POV B 603 " ideal model delta sigma weight residual 121.11 109.47 11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O13 POV E 602 " pdb=" P POV E 602 " pdb=" O14 POV E 602 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O13 POV D 503 " pdb=" P POV D 503 " pdb=" O14 POV D 503 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 ... (remaining 23925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 10468 31.02 - 62.05: 281 62.05 - 93.07: 88 93.07 - 124.10: 29 124.10 - 155.12: 6 Dihedral angle restraints: 10872 sinusoidal: 4892 harmonic: 5980 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual 180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2324 0.060 - 0.119: 406 0.119 - 0.179: 53 0.179 - 0.238: 7 0.238 - 0.298: 7 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2794 not shown) Planarity restraints: 2887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 TC9 E 601 " -0.014 2.00e-02 2.50e+03 1.05e-02 3.04e+00 pdb=" C22 TC9 E 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 E 601 " -0.012 2.00e-02 2.50e+03 pdb=" C24 TC9 E 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 E 601 " 0.000 2.00e-02 2.50e+03 pdb=" C27 TC9 E 601 " -0.002 2.00e-02 2.50e+03 pdb=" C28 TC9 E 601 " -0.016 2.00e-02 2.50e+03 pdb=" O29 TC9 E 601 " 0.014 2.00e-02 2.50e+03 pdb=" O40 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" O42 TC9 E 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 TC9 B 601 " -0.015 2.00e-02 2.50e+03 9.83e-03 2.66e+00 pdb=" C22 TC9 B 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 B 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 TC9 B 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C27 TC9 B 601 " -0.001 2.00e-02 2.50e+03 pdb=" C28 TC9 B 601 " -0.013 2.00e-02 2.50e+03 pdb=" O29 TC9 B 601 " 0.010 2.00e-02 2.50e+03 pdb=" O40 TC9 B 601 " -0.003 2.00e-02 2.50e+03 pdb=" O42 TC9 B 601 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ILE C 221 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE C 221 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL C 222 " 0.009 2.00e-02 2.50e+03 ... (remaining 2884 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 954 2.73 - 3.27: 16922 3.27 - 3.81: 28271 3.81 - 4.36: 34505 4.36 - 4.90: 59822 Nonbonded interactions: 140474 Sorted by model distance: nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.187 3.120 nonbonded pdb=" OG SER B 494 " pdb=" OD1 ASP B 496 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.211 3.120 nonbonded pdb=" OE2 GLU B 191 " pdb=" NH2 ARG B 222 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP C 138 " pdb=" NE2 GLN C 140 " model vdw 2.239 3.120 ... (remaining 140469 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 426) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426)) } ncs_group { reference = chain 'F' selection = chain 'I' 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.230 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.006 0.126 17548 Z= 0.283 Angle : 0.786 12.431 24004 Z= 0.344 Chirality : 0.049 0.298 2797 Planarity : 0.004 0.034 2882 Dihedral : 17.585 155.120 6957 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.21 (0.19), residues: 1995 helix: 2.85 (0.18), residues: 756 sheet: -0.69 (0.24), residues: 422 loop : -0.28 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 198 TYR 0.011 0.001 TYR B 439 PHE 0.014 0.001 PHE D 256 TRP 0.012 0.001 TRP D 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00621 (17521) covalent geometry : angle 0.77873 (23930) SS BOND : bond 0.01522 ( 7) SS BOND : angle 2.39316 ( 14) hydrogen bonds : bond 0.10184 ( 842) hydrogen bonds : angle 5.28261 ( 2673) link_ALPHA1-6 : bond 0.00291 ( 6) link_ALPHA1-6 : angle 1.70053 ( 18) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 2.15936 ( 27) link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 2.01893 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8312 (m-80) cc_final: 0.7897 (m-10) REVERT: D 226 SER cc_start: 0.8905 (m) cc_final: 0.8510 (p) REVERT: D 227 PHE cc_start: 0.7950 (t80) cc_final: 0.7200 (m-80) REVERT: D 325 PHE cc_start: 0.6617 (m-80) cc_final: 0.6397 (m-80) REVERT: E 317 LEU cc_start: 0.8513 (tp) cc_final: 0.8310 (tp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1107 time to fit residues: 26.2310 Evaluate side-chains 105 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN D 408 HIS E 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072154 restraints weight = 30145.709| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.53 r_work: 0.2745 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17548 Z= 0.145 Angle : 0.575 7.846 24004 Z= 0.275 Chirality : 0.044 0.190 2797 Planarity : 0.004 0.035 2882 Dihedral : 14.723 131.007 3048 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.32 % Allowed : 4.03 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.32 (0.19), residues: 1995 helix: 3.01 (0.18), residues: 762 sheet: -0.60 (0.25), residues: 411 loop : -0.36 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 198 TYR 0.011 0.001 TYR B 439 PHE 0.013 0.001 PHE D 256 TRP 0.012 0.001 TRP E 60 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00338 (17521) covalent geometry : angle 0.56508 (23930) SS BOND : bond 0.00729 ( 7) SS BOND : angle 1.81375 ( 14) hydrogen bonds : bond 0.04378 ( 842) hydrogen bonds : angle 4.26749 ( 2673) link_ALPHA1-6 : bond 0.00672 ( 6) link_ALPHA1-6 : angle 1.99969 ( 18) link_BETA1-4 : bond 0.00355 ( 9) link_BETA1-4 : angle 2.23637 ( 27) link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.53730 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.8912 (ttm) cc_final: 0.8681 (ttm) REVERT: C 293 PHE cc_start: 0.8803 (m-80) cc_final: 0.8375 (m-10) REVERT: D 227 PHE cc_start: 0.8343 (t80) cc_final: 0.7162 (m-80) REVERT: E 299 MET cc_start: 0.8278 (ttt) cc_final: 0.7926 (ttp) REVERT: E 317 LEU cc_start: 0.8254 (tp) cc_final: 0.8053 (tp) outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.1080 time to fit residues: 20.3605 Evaluate side-chains 103 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 105 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 0.1980 chunk 197 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 153 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.073139 restraints weight = 30207.825| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.55 r_work: 0.2772 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17548 Z= 0.120 Angle : 0.522 6.943 24004 Z= 0.251 Chirality : 0.043 0.188 2797 Planarity : 0.003 0.034 2882 Dihedral : 12.734 126.350 3048 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.48 % Allowed : 5.96 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1995 helix: 3.15 (0.18), residues: 761 sheet: -0.43 (0.25), residues: 391 loop : -0.33 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 198 TYR 0.010 0.001 TYR B 439 PHE 0.011 0.001 PHE D 325 TRP 0.012 0.001 TRP E 60 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00272 (17521) covalent geometry : angle 0.51344 (23930) SS BOND : bond 0.00682 ( 7) SS BOND : angle 1.54305 ( 14) hydrogen bonds : bond 0.04016 ( 842) hydrogen bonds : angle 3.99512 ( 2673) link_ALPHA1-6 : bond 0.00649 ( 6) link_ALPHA1-6 : angle 1.89510 ( 18) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.97660 ( 27) link_NAG-ASN : bond 0.00133 ( 5) link_NAG-ASN : angle 1.52588 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: C 133 MET cc_start: 0.8698 (ttm) cc_final: 0.8450 (ttm) REVERT: C 293 PHE cc_start: 0.8638 (m-80) cc_final: 0.8227 (m-10) REVERT: E 299 MET cc_start: 0.8010 (ttt) cc_final: 0.7594 (ttp) REVERT: E 317 LEU cc_start: 0.8309 (tp) cc_final: 0.8092 (tp) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.0976 time to fit residues: 19.0811 Evaluate side-chains 104 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.071615 restraints weight = 30231.276| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.54 r_work: 0.2750 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17548 Z= 0.165 Angle : 0.541 7.038 24004 Z= 0.261 Chirality : 0.044 0.204 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.947 129.311 3048 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.70 % Allowed : 7.35 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.50 (0.19), residues: 1995 helix: 3.13 (0.18), residues: 762 sheet: -0.37 (0.25), residues: 401 loop : -0.31 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.011 0.001 TYR B 439 PHE 0.010 0.001 PHE C 219 TRP 0.010 0.001 TRP D 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00392 (17521) covalent geometry : angle 0.53093 (23930) SS BOND : bond 0.00662 ( 7) SS BOND : angle 1.70231 ( 14) hydrogen bonds : bond 0.04093 ( 842) hydrogen bonds : angle 3.96975 ( 2673) link_ALPHA1-6 : bond 0.00650 ( 6) link_ALPHA1-6 : angle 1.95275 ( 18) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 2.16640 ( 27) link_NAG-ASN : bond 0.00153 ( 5) link_NAG-ASN : angle 1.58371 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8807 (m-80) cc_final: 0.8398 (m-10) REVERT: D 227 PHE cc_start: 0.8246 (t80) cc_final: 0.7260 (m-80) REVERT: D 243 MET cc_start: 0.9417 (mmm) cc_final: 0.9125 (mmp) REVERT: E 299 MET cc_start: 0.8321 (ttt) cc_final: 0.7950 (ttp) outliers start: 13 outliers final: 3 residues processed: 119 average time/residue: 0.1075 time to fit residues: 21.0887 Evaluate side-chains 106 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.070961 restraints weight = 30143.401| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.52 r_work: 0.2737 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17548 Z= 0.188 Angle : 0.553 7.478 24004 Z= 0.267 Chirality : 0.044 0.204 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.515 130.171 3048 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.59 % Allowed : 8.59 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1995 helix: 3.14 (0.18), residues: 761 sheet: -0.42 (0.25), residues: 403 loop : -0.30 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.012 0.001 TYR E 117 PHE 0.012 0.001 PHE D 256 TRP 0.011 0.001 TRP D 60 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00452 (17521) covalent geometry : angle 0.54312 (23930) SS BOND : bond 0.00647 ( 7) SS BOND : angle 1.94589 ( 14) hydrogen bonds : bond 0.04211 ( 842) hydrogen bonds : angle 3.97112 ( 2673) link_ALPHA1-6 : bond 0.00632 ( 6) link_ALPHA1-6 : angle 1.94212 ( 18) link_BETA1-4 : bond 0.00333 ( 9) link_BETA1-4 : angle 2.10063 ( 27) link_NAG-ASN : bond 0.00203 ( 5) link_NAG-ASN : angle 1.71487 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8806 (m-80) cc_final: 0.8392 (m-10) REVERT: D 227 PHE cc_start: 0.8262 (t80) cc_final: 0.7244 (m-80) REVERT: D 243 MET cc_start: 0.9421 (mmm) cc_final: 0.9133 (mmp) REVERT: E 299 MET cc_start: 0.8343 (ttt) cc_final: 0.7988 (ttp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.1095 time to fit residues: 19.7408 Evaluate side-chains 106 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 141 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 ASN E 313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.072646 restraints weight = 29798.668| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.55 r_work: 0.2768 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17548 Z= 0.118 Angle : 0.502 6.998 24004 Z= 0.243 Chirality : 0.043 0.184 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.166 131.030 3048 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.75 % Allowed : 8.96 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.63 (0.19), residues: 1995 helix: 3.28 (0.18), residues: 761 sheet: -0.31 (0.25), residues: 387 loop : -0.29 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.012 0.001 TYR E 117 PHE 0.015 0.001 PHE D 325 TRP 0.012 0.001 TRP E 60 HIS 0.005 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00271 (17521) covalent geometry : angle 0.49337 (23930) SS BOND : bond 0.00668 ( 7) SS BOND : angle 1.58104 ( 14) hydrogen bonds : bond 0.03842 ( 842) hydrogen bonds : angle 3.81894 ( 2673) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 1.76828 ( 18) link_BETA1-4 : bond 0.00410 ( 9) link_BETA1-4 : angle 1.78698 ( 27) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 1.54886 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7996 (ttm) REVERT: C 293 PHE cc_start: 0.8639 (m-80) cc_final: 0.8218 (m-10) REVERT: D 227 PHE cc_start: 0.8127 (t80) cc_final: 0.7125 (m-80) REVERT: D 243 MET cc_start: 0.9294 (mmm) cc_final: 0.9008 (mmp) REVERT: E 299 MET cc_start: 0.8075 (ttt) cc_final: 0.7555 (ttp) REVERT: E 467 PHE cc_start: 0.6975 (m-10) cc_final: 0.6355 (t80) outliers start: 14 outliers final: 5 residues processed: 118 average time/residue: 0.1100 time to fit residues: 21.1429 Evaluate side-chains 107 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 182 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.070962 restraints weight = 30072.064| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.52 r_work: 0.2735 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17548 Z= 0.194 Angle : 0.549 7.521 24004 Z= 0.265 Chirality : 0.044 0.192 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.153 130.002 3048 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.59 % Allowed : 9.29 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.54 (0.19), residues: 1995 helix: 3.17 (0.18), residues: 761 sheet: -0.35 (0.25), residues: 389 loop : -0.31 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.012 0.001 TYR B 439 PHE 0.011 0.001 PHE C 219 TRP 0.010 0.001 TRP A 311 HIS 0.007 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00466 (17521) covalent geometry : angle 0.53977 (23930) SS BOND : bond 0.00636 ( 7) SS BOND : angle 1.80527 ( 14) hydrogen bonds : bond 0.04149 ( 842) hydrogen bonds : angle 3.92184 ( 2673) link_ALPHA1-6 : bond 0.00631 ( 6) link_ALPHA1-6 : angle 1.86844 ( 18) link_BETA1-4 : bond 0.00318 ( 9) link_BETA1-4 : angle 2.09354 ( 27) link_NAG-ASN : bond 0.00238 ( 5) link_NAG-ASN : angle 1.68064 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.505 Fit side-chains REVERT: B 58 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8307 (ttm) REVERT: C 293 PHE cc_start: 0.8802 (m-80) cc_final: 0.8383 (m-10) REVERT: D 227 PHE cc_start: 0.8246 (t80) cc_final: 0.7218 (m-80) REVERT: D 243 MET cc_start: 0.9392 (mmm) cc_final: 0.9116 (mmp) REVERT: E 299 MET cc_start: 0.8360 (ttt) cc_final: 0.7889 (ttp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.1106 time to fit residues: 19.8436 Evaluate side-chains 105 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 1 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071978 restraints weight = 30148.854| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.54 r_work: 0.2757 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17548 Z= 0.132 Angle : 0.508 7.006 24004 Z= 0.246 Chirality : 0.043 0.183 2797 Planarity : 0.003 0.036 2882 Dihedral : 10.984 130.446 3048 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.48 % Allowed : 9.72 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.62 (0.19), residues: 1995 helix: 3.27 (0.18), residues: 761 sheet: -0.30 (0.25), residues: 387 loop : -0.29 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 198 TYR 0.012 0.001 TYR E 117 PHE 0.014 0.001 PHE D 325 TRP 0.012 0.001 TRP E 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00310 (17521) covalent geometry : angle 0.50020 (23930) SS BOND : bond 0.00659 ( 7) SS BOND : angle 1.57149 ( 14) hydrogen bonds : bond 0.03901 ( 842) hydrogen bonds : angle 3.83772 ( 2673) link_ALPHA1-6 : bond 0.00727 ( 6) link_ALPHA1-6 : angle 1.71571 ( 18) link_BETA1-4 : bond 0.00392 ( 9) link_BETA1-4 : angle 1.81335 ( 27) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 1.55546 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.543 Fit side-chains REVERT: B 58 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8196 (ttm) REVERT: C 293 PHE cc_start: 0.8794 (m-80) cc_final: 0.8379 (m-10) REVERT: D 227 PHE cc_start: 0.8082 (t80) cc_final: 0.7199 (m-80) REVERT: D 243 MET cc_start: 0.9346 (mmm) cc_final: 0.9086 (mmp) REVERT: E 299 MET cc_start: 0.8350 (ttt) cc_final: 0.7883 (ttp) REVERT: E 467 PHE cc_start: 0.7079 (m-10) cc_final: 0.6307 (t80) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.1137 time to fit residues: 20.1686 Evaluate side-chains 107 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.072553 restraints weight = 29804.133| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.54 r_work: 0.2767 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17548 Z= 0.122 Angle : 0.508 7.410 24004 Z= 0.246 Chirality : 0.042 0.183 2797 Planarity : 0.003 0.036 2882 Dihedral : 10.850 131.399 3048 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.64 % Allowed : 9.50 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.66 (0.19), residues: 1995 helix: 3.29 (0.18), residues: 761 sheet: -0.26 (0.25), residues: 387 loop : -0.27 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.011 0.001 TYR B 439 PHE 0.010 0.001 PHE C 219 TRP 0.012 0.001 TRP E 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00283 (17521) covalent geometry : angle 0.50026 (23930) SS BOND : bond 0.00663 ( 7) SS BOND : angle 1.51839 ( 14) hydrogen bonds : bond 0.03822 ( 842) hydrogen bonds : angle 3.79240 ( 2673) link_ALPHA1-6 : bond 0.00722 ( 6) link_ALPHA1-6 : angle 1.66833 ( 18) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 1.78653 ( 27) link_NAG-ASN : bond 0.00153 ( 5) link_NAG-ASN : angle 1.51565 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.597 Fit side-chains REVERT: C 293 PHE cc_start: 0.8780 (m-80) cc_final: 0.8379 (m-10) REVERT: D 227 PHE cc_start: 0.8045 (t80) cc_final: 0.7102 (m-80) REVERT: E 299 MET cc_start: 0.8334 (ttt) cc_final: 0.7864 (ttp) REVERT: E 467 PHE cc_start: 0.7098 (m-10) cc_final: 0.6367 (t80) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.1082 time to fit residues: 19.7059 Evaluate side-chains 109 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 186 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074049 restraints weight = 29592.773| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.53 r_work: 0.2796 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17548 Z= 0.102 Angle : 0.485 6.908 24004 Z= 0.236 Chirality : 0.042 0.183 2797 Planarity : 0.003 0.036 2882 Dihedral : 10.747 136.096 3048 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.74 (0.19), residues: 1995 helix: 3.39 (0.18), residues: 761 sheet: -0.20 (0.25), residues: 385 loop : -0.27 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.010 0.001 TYR B 439 PHE 0.016 0.001 PHE D 325 TRP 0.013 0.001 TRP D 60 HIS 0.005 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00229 (17521) covalent geometry : angle 0.47853 (23930) SS BOND : bond 0.00674 ( 7) SS BOND : angle 1.39053 ( 14) hydrogen bonds : bond 0.03589 ( 842) hydrogen bonds : angle 3.68467 ( 2673) link_ALPHA1-6 : bond 0.00713 ( 6) link_ALPHA1-6 : angle 1.54503 ( 18) link_BETA1-4 : bond 0.00459 ( 9) link_BETA1-4 : angle 1.62315 ( 27) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 1.44686 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.631 Fit side-chains REVERT: C 293 PHE cc_start: 0.8765 (m-80) cc_final: 0.8361 (m-10) REVERT: E 299 MET cc_start: 0.8330 (ttt) cc_final: 0.7866 (ttp) REVERT: E 467 PHE cc_start: 0.7107 (m-10) cc_final: 0.6465 (t80) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.1116 time to fit residues: 21.3597 Evaluate side-chains 110 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073717 restraints weight = 29821.987| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.54 r_work: 0.2790 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17548 Z= 0.116 Angle : 0.499 6.956 24004 Z= 0.243 Chirality : 0.042 0.210 2797 Planarity : 0.003 0.036 2882 Dihedral : 10.695 135.636 3048 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.64 % Allowed : 10.20 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.77 (0.19), residues: 1995 helix: 3.38 (0.18), residues: 760 sheet: -0.15 (0.26), residues: 385 loop : -0.23 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.010 0.001 TYR B 439 PHE 0.023 0.001 PHE D 227 TRP 0.012 0.001 TRP A 311 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00268 (17521) covalent geometry : angle 0.49197 (23930) SS BOND : bond 0.00661 ( 7) SS BOND : angle 1.45142 ( 14) hydrogen bonds : bond 0.03643 ( 842) hydrogen bonds : angle 3.69220 ( 2673) link_ALPHA1-6 : bond 0.00667 ( 6) link_ALPHA1-6 : angle 1.56398 ( 18) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 1.70494 ( 27) link_NAG-ASN : bond 0.00149 ( 5) link_NAG-ASN : angle 1.47832 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3495.53 seconds wall clock time: 60 minutes 48.92 seconds (3648.92 seconds total)