Starting phenix.real_space_refine on Sat Jul 4 02:43:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sms_25207/07_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_25207/07_2026/7sms_25207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sms_25207/07_2026/7sms_25207.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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: 3.21, per 1000 atoms: 0.19 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: 1.66 Conformation dependent library (CDL) restraints added in 702.5 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: 0.51 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: 2.98 Time building geometry restraints manager: 2.12 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: 9853 31.02 - 62.05: 247 62.05 - 93.07: 33 93.07 - 124.10: 7 124.10 - 155.12: 6 Dihedral angle restraints: 10146 sinusoidal: 4166 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 10143 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: 1.070 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.530 Find NCS groups from input model: 0.250 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:1.200 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 15.178 155.120 6231 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/Z covalent geometry : bond 0.00621 / 0.28 (17521) covalent geometry : angle 0.77873 / 0.34 (23930) SS BOND : bond 0.01522 / 1.17 ( 7) SS BOND : angle 2.39316 / 1.32 ( 14) hydrogen bonds : bond 0.10184 / 7.35 ( 842) hydrogen bonds : angle 5.28261 / 3.80 ( 2673) link_ALPHA1-6 : bond 0.00291 / 0.15 ( 6) link_ALPHA1-6 : angle 1.70053 / 1.08 ( 18) link_BETA1-4 : bond 0.00399 / 0.28 ( 9) link_BETA1-4 : angle 2.15936 / 1.32 ( 27) link_NAG-ASN : bond 0.00245 / 0.12 ( 5) link_NAG-ASN : angle 2.01893 / 1.10 ( 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 : 0.677 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: 0.1225 time to fit residues: 28.9870 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 : 0.688 ------------------------------------------------------------------------------- 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... ** 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 = 0.3264 r_free = 0.3264 target = 0.093903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.072055 restraints weight = 30157.187| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.54 r_work: 0.2742 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 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 = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0842 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= 0.145 Angle : 0.564 8.209 24004 Z= 0.272 Chirality : 0.043 0.187 2797 Planarity : 0.004 0.034 2882 Dihedral : 11.399 131.472 2322 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.38 % Allowed : 3.81 % Favored : 95.81 % 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: 1.31 (0.19), residues: 1995 helix: 3.00 (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/Z covalent geometry : bond 0.00338 / 0.14 (17521) covalent geometry : angle 0.55716 / 0.27 (23930) SS BOND : bond 0.00732 / 0.36 ( 7) SS BOND : angle 1.80157 / 1.01 ( 14) hydrogen bonds : bond 0.04420 / 3.00 ( 842) hydrogen bonds : angle 4.29715 / 3.09 ( 2673) link_ALPHA1-6 : bond 0.00517 / 0.28 ( 6) link_ALPHA1-6 : angle 1.62082 / 1.04 ( 18) link_BETA1-4 : bond 0.00324 / 0.22 ( 9) link_BETA1-4 : angle 1.72362 / 1.18 ( 27) link_NAG-ASN : bond 0.00107 / 0.06 ( 5) link_NAG-ASN : angle 1.56325 / 0.86 ( 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: 7 poor density : 111 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.8910 (ttm) cc_final: 0.8676 (ttm) REVERT: C 293 PHE cc_start: 0.8802 (m-80) cc_final: 0.8374 (m-10) REVERT: D 227 PHE cc_start: 0.8355 (t80) cc_final: 0.7176 (m-80) REVERT: E 299 MET cc_start: 0.8280 (ttt) cc_final: 0.7924 (ttp) outliers start: 7 outliers final: 4 residues processed: 114 average time/residue: 0.1143 time to fit residues: 21.4346 Evaluate side-chains 104 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 0.5980 chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 267 GLN ** 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 = 0.3255 r_free = 0.3255 target = 0.093353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071532 restraints weight = 30321.754| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.54 r_work: 0.2747 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17548 Z= 0.162 Angle : 0.542 7.163 24004 Z= 0.262 Chirality : 0.043 0.189 2797 Planarity : 0.003 0.034 2882 Dihedral : 10.538 124.312 2322 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.75 % Allowed : 5.90 % Favored : 93.34 % 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: 1.40 (0.19), residues: 1995 helix: 3.08 (0.18), residues: 761 sheet: -0.50 (0.25), residues: 399 loop : -0.35 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 198 TYR 0.011 0.001 TYR B 439 PHE 0.011 0.001 PHE D 325 TRP 0.012 0.001 TRP E 60 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (17521) covalent geometry : angle 0.53440 / 0.26 (23930) SS BOND : bond 0.00673 / 0.33 ( 7) SS BOND : angle 1.71296 / 0.96 ( 14) hydrogen bonds : bond 0.04228 / 2.86 ( 842) hydrogen bonds : angle 4.07654 / 2.93 ( 2673) link_ALPHA1-6 : bond 0.00433 / 0.24 ( 6) link_ALPHA1-6 : angle 1.66631 / 1.06 ( 18) link_BETA1-4 : bond 0.00408 / 0.29 ( 9) link_BETA1-4 : angle 1.81216 / 1.19 ( 27) link_NAG-ASN : bond 0.00176 / 0.09 ( 5) link_NAG-ASN : angle 1.59332 / 0.89 ( 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 121 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8808 (m-80) cc_final: 0.8393 (m-10) REVERT: D 243 MET cc_start: 0.9417 (mmm) cc_final: 0.9152 (mmp) REVERT: E 299 MET cc_start: 0.8302 (ttt) cc_final: 0.7921 (ttp) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.1160 time to fit residues: 21.5338 Evaluate side-chains 110 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 58 MET 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 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 D residue 426 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 267 GLN C 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072983 restraints weight = 30000.297| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.55 r_work: 0.2775 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1256 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= 0.115 Angle : 0.499 6.942 24004 Z= 0.244 Chirality : 0.042 0.185 2797 Planarity : 0.003 0.035 2882 Dihedral : 10.046 129.785 2322 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.59 % Allowed : 7.46 % 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: 1.55 (0.19), residues: 1995 helix: 3.22 (0.18), residues: 761 sheet: -0.39 (0.25), residues: 400 loop : -0.31 (0.22), residues: 834 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 0.009 0.001 PHE C 219 TRP 0.011 0.001 TRP A 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17521) covalent geometry : angle 0.49280 / 0.24 (23930) SS BOND : bond 0.00676 / 0.33 ( 7) SS BOND : angle 1.49804 / 0.80 ( 14) hydrogen bonds : bond 0.03900 / 2.63 ( 842) hydrogen bonds : angle 3.90446 / 2.80 ( 2673) link_ALPHA1-6 : bond 0.00513 / 0.28 ( 6) link_ALPHA1-6 : angle 1.55424 / 0.99 ( 18) link_BETA1-4 : bond 0.00373 / 0.25 ( 9) link_BETA1-4 : angle 1.57984 / 1.08 ( 27) link_NAG-ASN : bond 0.00114 / 0.06 ( 5) link_NAG-ASN : angle 1.44810 / 0.80 ( 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: 11 poor density : 112 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: C 133 MET cc_start: 0.8677 (ttm) cc_final: 0.8434 (ttm) REVERT: C 293 PHE cc_start: 0.8633 (m-80) cc_final: 0.8222 (m-10) REVERT: D 227 PHE cc_start: 0.8188 (t80) cc_final: 0.7244 (m-80) REVERT: D 243 MET cc_start: 0.9329 (mmm) cc_final: 0.9053 (mmp) REVERT: D 278 MET cc_start: 0.8316 (tpp) cc_final: 0.8096 (tpp) REVERT: E 299 MET cc_start: 0.8021 (ttt) cc_final: 0.7623 (ttp) outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 0.1191 time to fit residues: 22.8785 Evaluate side-chains 104 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.072386 restraints weight = 30021.025| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.54 r_work: 0.2766 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1340 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= 0.135 Angle : 0.508 6.963 24004 Z= 0.248 Chirality : 0.042 0.185 2797 Planarity : 0.003 0.035 2882 Dihedral : 9.749 131.474 2322 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.54 % Allowed : 8.43 % Favored : 91.04 % 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: 1.61 (0.19), residues: 1995 helix: 3.25 (0.18), residues: 761 sheet: -0.29 (0.25), residues: 387 loop : -0.31 (0.22), residues: 847 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 0.011 0.001 TRP E 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (17521) covalent geometry : angle 0.50114 / 0.25 (23930) SS BOND : bond 0.00653 / 0.32 ( 7) SS BOND : angle 1.69335 / 0.93 ( 14) hydrogen bonds : bond 0.03901 / 2.62 ( 842) hydrogen bonds : angle 3.86428 / 2.78 ( 2673) link_ALPHA1-6 : bond 0.00444 / 0.25 ( 6) link_ALPHA1-6 : angle 1.60370 / 1.02 ( 18) link_BETA1-4 : bond 0.00343 / 0.24 ( 9) link_BETA1-4 : angle 1.64705 / 1.10 ( 27) link_NAG-ASN : bond 0.00107 / 0.05 ( 5) link_NAG-ASN : angle 1.52337 / 0.83 ( 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 116 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8207 (ttm) REVERT: C 133 MET cc_start: 0.8882 (ttm) cc_final: 0.8657 (ttm) REVERT: C 293 PHE cc_start: 0.8786 (m-80) cc_final: 0.8373 (m-10) REVERT: D 227 PHE cc_start: 0.8289 (t80) cc_final: 0.7278 (m-80) REVERT: D 243 MET cc_start: 0.9360 (mmm) cc_final: 0.9070 (mmp) REVERT: E 299 MET cc_start: 0.8307 (ttt) cc_final: 0.7948 (ttp) REVERT: E 467 PHE cc_start: 0.7109 (m-10) cc_final: 0.6333 (t80) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.1158 time to fit residues: 20.6317 Evaluate side-chains 106 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET 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 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071641 restraints weight = 29873.075| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.53 r_work: 0.2752 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 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 = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17548 Z= 0.161 Angle : 0.521 7.052 24004 Z= 0.254 Chirality : 0.043 0.189 2797 Planarity : 0.003 0.035 2882 Dihedral : 9.553 132.204 2322 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.64 % Allowed : 9.02 % Favored : 90.34 % 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: 1.60 (0.19), residues: 1995 helix: 3.24 (0.18), residues: 761 sheet: -0.33 (0.25), residues: 389 loop : -0.29 (0.22), residues: 845 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 D 256 TRP 0.010 0.001 TRP A 311 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (17521) covalent geometry : angle 0.51315 / 0.25 (23930) SS BOND : bond 0.00647 / 0.32 ( 7) SS BOND : angle 1.76968 / 0.98 ( 14) hydrogen bonds : bond 0.04004 / 2.70 ( 842) hydrogen bonds : angle 3.87444 / 2.79 ( 2673) link_ALPHA1-6 : bond 0.00396 / 0.22 ( 6) link_ALPHA1-6 : angle 1.63120 / 1.03 ( 18) link_BETA1-4 : bond 0.00295 / 0.21 ( 9) link_BETA1-4 : angle 1.72357 / 1.14 ( 27) link_NAG-ASN : bond 0.00185 / 0.10 ( 5) link_NAG-ASN : angle 1.62325 / 0.89 ( 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 121 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 LEU cc_start: 0.7732 (mt) cc_final: 0.7528 (mm) REVERT: B 58 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: C 293 PHE cc_start: 0.8786 (m-80) cc_final: 0.8371 (m-10) REVERT: D 227 PHE cc_start: 0.8274 (t80) cc_final: 0.7262 (m-80) REVERT: D 243 MET cc_start: 0.9369 (mmm) cc_final: 0.9087 (mmp) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 0.1142 time to fit residues: 21.1994 Evaluate side-chains 106 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 76 optimal weight: 1.9990 chunk 174 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 135 optimal weight: 0.6980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN ** C 312 HIS ** 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 = 0.3277 r_free = 0.3277 target = 0.094731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.072982 restraints weight = 29794.180| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.54 r_work: 0.2778 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1524 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= 0.114 Angle : 0.490 6.898 24004 Z= 0.239 Chirality : 0.042 0.183 2797 Planarity : 0.003 0.035 2882 Dihedral : 9.360 133.369 2322 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.59 % Allowed : 9.23 % Favored : 90.18 % 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: 1.70 (0.19), residues: 1995 helix: 3.34 (0.18), residues: 761 sheet: -0.25 (0.25), residues: 387 loop : -0.26 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.010 0.001 TYR B 439 PHE 0.015 0.001 PHE D 325 TRP 0.011 0.001 TRP E 60 HIS 0.005 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17521) covalent geometry : angle 0.48350 / 0.24 (23930) SS BOND : bond 0.00661 / 0.33 ( 7) SS BOND : angle 1.49073 / 0.80 ( 14) hydrogen bonds : bond 0.03752 / 2.51 ( 842) hydrogen bonds : angle 3.76843 / 2.71 ( 2673) link_ALPHA1-6 : bond 0.00475 / 0.26 ( 6) link_ALPHA1-6 : angle 1.52785 / 0.97 ( 18) link_BETA1-4 : bond 0.00363 / 0.24 ( 9) link_BETA1-4 : angle 1.55822 / 1.06 ( 27) link_NAG-ASN : bond 0.00111 / 0.06 ( 5) link_NAG-ASN : angle 1.47350 / 0.80 ( 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 118 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7965 (ttm) REVERT: C 293 PHE cc_start: 0.8618 (m-80) cc_final: 0.8207 (m-10) REVERT: D 227 PHE cc_start: 0.8070 (t80) cc_final: 0.7014 (m-80) REVERT: E 299 MET cc_start: 0.8049 (ttt) cc_final: 0.7531 (ttp) REVERT: E 467 PHE cc_start: 0.6908 (m-10) cc_final: 0.6335 (t80) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.0988 time to fit residues: 18.3566 Evaluate side-chains 108 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 1 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 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: 0.4980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3283 r_free = 0.3283 target = 0.095114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073413 restraints weight = 30027.339| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.55 r_work: 0.2786 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1611 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= 0.111 Angle : 0.487 6.866 24004 Z= 0.237 Chirality : 0.041 0.183 2797 Planarity : 0.003 0.035 2882 Dihedral : 9.216 133.896 2322 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.59 % Allowed : 9.61 % 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: 1.74 (0.19), residues: 1995 helix: 3.39 (0.18), residues: 760 sheet: -0.22 (0.25), residues: 384 loop : -0.26 (0.22), residues: 851 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 0.008 0.001 PHE C 219 TRP 0.011 0.001 TRP E 60 HIS 0.004 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17521) covalent geometry : angle 0.48017 / 0.24 (23930) SS BOND : bond 0.00659 / 0.32 ( 7) SS BOND : angle 1.49087 / 0.80 ( 14) hydrogen bonds : bond 0.03656 / 2.45 ( 842) hydrogen bonds : angle 3.71063 / 2.67 ( 2673) link_ALPHA1-6 : bond 0.00453 / 0.25 ( 6) link_ALPHA1-6 : angle 1.53701 / 0.98 ( 18) link_BETA1-4 : bond 0.00351 / 0.23 ( 9) link_BETA1-4 : angle 1.56650 / 1.05 ( 27) link_NAG-ASN : bond 0.00118 / 0.06 ( 5) link_NAG-ASN : angle 1.44544 / 0.79 ( 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 119 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: C 133 MET cc_start: 0.8722 (ttm) cc_final: 0.8505 (ttm) REVERT: C 293 PHE cc_start: 0.8609 (m-80) cc_final: 0.8204 (m-10) REVERT: D 227 PHE cc_start: 0.8038 (t80) cc_final: 0.6976 (m-80) REVERT: D 408 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6595 (t-90) REVERT: E 299 MET cc_start: 0.8068 (ttt) cc_final: 0.7553 (ttp) REVERT: E 467 PHE cc_start: 0.6977 (m-10) cc_final: 0.6403 (t80) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.1133 time to fit residues: 21.0753 Evaluate side-chains 108 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 D residue 408 HIS Chi-restraints excluded: chain E residue 317 LEU 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: 2.9990 chunk 196 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 276 GLN ** C 312 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.094240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.072454 restraints weight = 29876.653| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.54 r_work: 0.2766 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17548 Z= 0.148 Angle : 0.510 7.078 24004 Z= 0.248 Chirality : 0.042 0.182 2797 Planarity : 0.003 0.035 2882 Dihedral : 9.167 133.818 2322 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.70 % Allowed : 9.88 % Favored : 89.43 % 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: 1.70 (0.19), residues: 1995 helix: 3.32 (0.18), residues: 760 sheet: -0.20 (0.25), residues: 391 loop : -0.27 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.011 0.001 TYR B 439 PHE 0.014 0.001 PHE D 325 TRP 0.010 0.001 TRP A 311 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (17521) covalent geometry : angle 0.50249 / 0.25 (23930) SS BOND : bond 0.00637 / 0.31 ( 7) SS BOND : angle 1.61219 / 0.89 ( 14) hydrogen bonds : bond 0.03824 / 2.56 ( 842) hydrogen bonds : angle 3.76547 / 2.71 ( 2673) link_ALPHA1-6 : bond 0.00374 / 0.21 ( 6) link_ALPHA1-6 : angle 1.58896 / 1.01 ( 18) link_BETA1-4 : bond 0.00304 / 0.21 ( 9) link_BETA1-4 : angle 1.67079 / 1.10 ( 27) link_NAG-ASN : bond 0.00162 / 0.08 ( 5) link_NAG-ASN : angle 1.52341 / 0.83 ( 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 114 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: C 293 PHE cc_start: 0.8776 (m-80) cc_final: 0.8373 (m-10) REVERT: D 227 PHE cc_start: 0.8121 (t80) cc_final: 0.7009 (m-80) REVERT: D 408 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6688 (t-90) REVERT: E 299 MET cc_start: 0.8312 (ttt) cc_final: 0.7837 (ttp) REVERT: E 467 PHE cc_start: 0.7076 (m-10) cc_final: 0.6345 (t80) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.1058 time to fit residues: 18.7502 Evaluate side-chains 110 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 122 optimal weight: 0.0070 chunk 186 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072815 restraints weight = 29674.415| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.53 r_work: 0.2774 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17548 Z= 0.127 Angle : 0.495 6.925 24004 Z= 0.241 Chirality : 0.042 0.181 2797 Planarity : 0.003 0.036 2882 Dihedral : 9.068 133.965 2322 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.54 % Allowed : 10.14 % Favored : 89.32 % 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: 1.72 (0.19), residues: 1995 helix: 3.35 (0.18), residues: 760 sheet: -0.18 (0.25), residues: 384 loop : -0.27 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.011 0.001 TYR E 117 PHE 0.012 0.001 PHE C 219 TRP 0.011 0.001 TRP E 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (17521) covalent geometry : angle 0.48787 / 0.24 (23930) SS BOND : bond 0.00649 / 0.32 ( 7) SS BOND : angle 1.53382 / 0.83 ( 14) hydrogen bonds : bond 0.03742 / 2.51 ( 842) hydrogen bonds : angle 3.73613 / 2.69 ( 2673) link_ALPHA1-6 : bond 0.00419 / 0.23 ( 6) link_ALPHA1-6 : angle 1.54569 / 0.98 ( 18) link_BETA1-4 : bond 0.00319 / 0.21 ( 9) link_BETA1-4 : angle 1.61360 / 1.08 ( 27) link_NAG-ASN : bond 0.00138 / 0.07 ( 5) link_NAG-ASN : angle 1.48958 / 0.81 ( 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 111 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 58 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: B 276 GLN cc_start: 0.8247 (tp40) cc_final: 0.7984 (tt0) REVERT: C 293 PHE cc_start: 0.8764 (m-80) cc_final: 0.8355 (m-10) REVERT: D 408 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.6670 (t-90) REVERT: E 299 MET cc_start: 0.8314 (ttt) cc_final: 0.7840 (ttp) REVERT: E 467 PHE cc_start: 0.7063 (m-10) cc_final: 0.6358 (t80) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.1147 time to fit residues: 20.0471 Evaluate side-chains 109 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.072366 restraints weight = 30001.210| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.55 r_work: 0.2765 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 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 = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17548 Z= 0.141 Angle : 0.506 7.892 24004 Z= 0.246 Chirality : 0.042 0.181 2797 Planarity : 0.003 0.036 2882 Dihedral : 8.994 133.679 2322 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.64 % Allowed : 10.14 % Favored : 89.21 % 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: 1.71 (0.19), residues: 1995 helix: 3.32 (0.18), residues: 760 sheet: -0.18 (0.25), residues: 391 loop : -0.26 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.011 0.001 TYR B 439 PHE 0.012 0.001 PHE C 455 TRP 0.010 0.001 TRP A 311 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17521) covalent geometry : angle 0.49847 / 0.24 (23930) SS BOND : bond 0.00644 / 0.32 ( 7) SS BOND : angle 1.59983 / 0.88 ( 14) hydrogen bonds : bond 0.03802 / 2.55 ( 842) hydrogen bonds : angle 3.75583 / 2.70 ( 2673) link_ALPHA1-6 : bond 0.00392 / 0.22 ( 6) link_ALPHA1-6 : angle 1.57236 / 1.00 ( 18) link_BETA1-4 : bond 0.00299 / 0.21 ( 9) link_BETA1-4 : angle 1.66543 / 1.10 ( 27) link_NAG-ASN : bond 0.00160 / 0.08 ( 5) link_NAG-ASN : angle 1.52896 / 0.83 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.67 seconds wall clock time: 59 minutes 39.31 seconds (3579.31 seconds total)