Starting phenix.real_space_refine on Tue Aug 26 19:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmk_47008/08_2025/9dmk_47008.map" } resolution = 2.46 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= 0.020 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 90 5.16 5 C 13152 2.51 5 N 3253 2.21 5 O 3764 1.98 5 H 19781 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40043 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6433 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6486 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6575 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7055 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6480 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3226 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3307 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 200} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.31, per 1000 atoms: 0.18 Number of scatterers: 40043 At special positions: 0 Unit cell: (100.045, 149.6, 203.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 3 15.00 O 3764 8.00 N 3253 7.00 C 13152 6.00 H 19781 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 180 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 112 " distance=2.04 Simple disulfide: pdb=" SG CYS G 158 " - pdb=" SG CYS G 218 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 5 " BETA1-4 " 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG G 301 " - " ASN G 45 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN E 141 " " NAG K 1 " - " ASN D 143 " " NAG L 1 " - " ASN B 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 30 sheets defined 37.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.228A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.921A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.964A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.731A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 436 removed outlier: 3.534A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.059A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 231 removed outlier: 3.568A pdb=" N CYS C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 241 through 264 removed outlier: 4.107A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 369 through 436 removed outlier: 3.577A pdb=" N PHE C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 272 Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.808A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 248 removed outlier: 3.555A pdb=" N PHE D 247 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.652A pdb=" N VAL D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.714A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.806A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 238 removed outlier: 4.079A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.862A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.894A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.579A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 removed outlier: 3.799A pdb=" N GLN F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 96' Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 196 through 198 No H-bonds generated for 'chain 'F' and resid 196 through 198' Processing helix chain 'F' and resid 227 through 230 removed outlier: 3.712A pdb=" N GLY F 230 " --> pdb=" O SER F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 207 through 213 removed outlier: 3.523A pdb=" N GLU G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 207 through 213' Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.001A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.001A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 49 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.691A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.278A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.278A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 49 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 42 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN C 53 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL C 61 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C 30 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.764A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.217A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.217A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER E 42 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU E 40 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS E 53 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR E 61 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG E 30 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.913A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.129A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.129A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.822A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.676A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.676A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.170A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.170A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 34 through 37 Processing sheet with id=AC3, first strand: chain 'F' and resid 41 through 43 removed outlier: 6.979A pdb=" N ILE F 65 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY F 81 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP F 67 " --> pdb=" O MET F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 43 Processing sheet with id=AC5, first strand: chain 'F' and resid 160 through 164 removed outlier: 3.545A pdb=" N LYS F 183 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 179 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 220 " --> pdb=" O CYS F 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR F 216 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 221 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 160 through 164 removed outlier: 3.545A pdb=" N LYS F 183 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 179 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 220 " --> pdb=" O CYS F 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR F 216 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 190 through 194 removed outlier: 4.490A pdb=" N CYS F 236 " --> pdb=" O LYS F 249 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 249 " --> pdb=" O CYS F 236 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AC9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.441A pdb=" N LEU G 57 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR G 73 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.947A pdb=" N THR G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 138 through 142 removed outlier: 3.880A pdb=" N ALA G 154 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 205 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL G 156 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 172 through 173 removed outlier: 3.798A pdb=" N ALA G 217 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS G 218 " --> pdb=" O LYS G 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS G 231 " --> pdb=" O CYS G 218 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3159 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: 10.62 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19762 1.04 - 1.23: 347 1.23 - 1.43: 8275 1.43 - 1.62: 12029 1.62 - 1.82: 141 Bond restraints: 40554 Sorted by residual: bond pdb=" NZ LYS C 77 " pdb=" HZ1 LYS C 77 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" NZ LYS B 167 " pdb=" HZ1 LYS B 167 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS E 10 " pdb=" HZ3 LYS E 10 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS D 19 " pdb=" HZ1 LYS D 19 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS F 249 " pdb=" HZ2 LYS F 249 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 40549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.16: 73253 13.16 - 26.32: 5 26.32 - 39.48: 3 39.48 - 52.64: 1 52.64 - 65.79: 3 Bond angle restraints: 73265 Sorted by residual: angle pdb=" CA GLY F 174 " pdb=" N GLY F 174 " pdb=" H GLY F 174 " ideal model delta sigma weight residual 114.00 179.79 -65.79 3.00e+00 1.11e-01 4.81e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 171.03 -57.03 3.00e+00 1.11e-01 3.61e+02 angle pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" H LYS A 368 " ideal model delta sigma weight residual 114.00 169.22 -55.22 3.00e+00 1.11e-01 3.39e+02 angle pdb=" CA LEU C 366 " pdb=" N LEU C 366 " pdb=" H LEU C 366 " ideal model delta sigma weight residual 114.00 157.96 -43.96 3.00e+00 1.11e-01 2.15e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 149.12 -35.12 3.00e+00 1.11e-01 1.37e+02 ... (remaining 73260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 18547 25.63 - 51.27: 895 51.27 - 76.90: 174 76.90 - 102.54: 48 102.54 - 128.17: 15 Dihedral angle restraints: 19679 sinusoidal: 10939 harmonic: 8740 Sorted by residual: dihedral pdb=" C PHE A 325 " pdb=" N PHE A 325 " pdb=" CA PHE A 325 " pdb=" CB PHE A 325 " ideal model delta harmonic sigma weight residual -122.60 -165.01 42.41 0 2.50e+00 1.60e-01 2.88e+02 dihedral pdb=" N PHE A 325 " pdb=" C PHE A 325 " pdb=" CA PHE A 325 " pdb=" CB PHE A 325 " ideal model delta harmonic sigma weight residual 122.80 162.78 -39.98 0 2.50e+00 1.60e-01 2.56e+02 dihedral pdb=" CD ARG A 301 " pdb=" NE ARG A 301 " pdb=" CZ ARG A 301 " pdb=" NH1 ARG A 301 " ideal model delta sinusoidal sigma weight residual 0.00 69.98 -69.98 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 19676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 3318 0.352 - 0.703: 1 0.703 - 1.055: 1 1.055 - 1.406: 0 1.406 - 1.758: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.20 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.88e+01 chirality pdb=" CA PHE A 325 " pdb=" N PHE A 325 " pdb=" C PHE A 325 " pdb=" CB PHE A 325 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.73e+01 ... (remaining 3318 not shown) Planarity restraints: 5829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 132 " 0.755 9.50e-02 1.11e+02 3.44e-01 1.31e+03 pdb=" NE ARG G 132 " 0.169 2.00e-02 2.50e+03 pdb=" CZ ARG G 132 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG G 132 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 132 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG G 132 " -0.496 2.00e-02 2.50e+03 pdb="HH12 ARG G 132 " 0.452 2.00e-02 2.50e+03 pdb="HH21 ARG G 132 " -0.085 2.00e-02 2.50e+03 pdb="HH22 ARG G 132 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 301 " -0.186 2.00e-02 2.50e+03 1.60e-01 3.19e+02 pdb=" C7 NAG G 301 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG G 301 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG G 301 " 0.266 2.00e-02 2.50e+03 pdb=" O7 NAG G 301 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 182 " -0.654 9.50e-02 1.11e+02 2.37e-01 2.47e+02 pdb=" NE ARG C 182 " -0.081 2.00e-02 2.50e+03 pdb=" CZ ARG C 182 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 182 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 182 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 182 " 0.200 2.00e-02 2.50e+03 pdb="HH12 ARG C 182 " -0.159 2.00e-02 2.50e+03 pdb="HH21 ARG C 182 " 0.082 2.00e-02 2.50e+03 pdb="HH22 ARG C 182 " -0.006 2.00e-02 2.50e+03 ... (remaining 5826 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 597 2.11 - 2.73: 68409 2.73 - 3.35: 112890 3.35 - 3.98: 151266 3.98 - 4.60: 234083 Nonbonded interactions: 567245 Sorted by model distance: nonbonded pdb=" O ASN D 187 " pdb=" HZ1 LYS D 224 " model vdw 1.485 2.450 nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.495 2.100 nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.523 2.100 nonbonded pdb=" HE1 PHE D 241 " pdb=" HG1 THR D 464 " model vdw 1.534 2.100 nonbonded pdb="HD21 ASN C 310 " pdb=" HZ2 LYS C 314 " model vdw 1.551 2.100 ... (remaining 567240 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 436) selection = (chain 'C' and (resid 1 through 330 or resid 369 through 436)) } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 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: 0.230 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 37.350 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.008 0.807 20807 Z= 0.639 Angle : 0.880 17.171 28399 Z= 0.479 Chirality : 0.062 1.758 3321 Planarity : 0.014 0.465 3503 Dihedral : 16.805 128.172 8042 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 0.45 % Allowed : 13.74 % Favored : 85.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.07 (0.17), residues: 2451 helix: 2.26 (0.18), residues: 794 sheet: 0.07 (0.21), residues: 577 loop : -0.01 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 429 TYR 0.016 0.001 TYR F 185 PHE 0.019 0.002 PHE C 256 TRP 0.015 0.001 TRP F 194 HIS 0.015 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00542 (20773) covalent geometry : angle 0.85007 (28310) SS BOND : bond 0.00694 ( 10) SS BOND : angle 1.25932 ( 20) hydrogen bonds : bond 0.15463 ( 1002) hydrogen bonds : angle 6.53852 ( 3159) Misc. bond : bond 0.80669 ( 1) link_ALPHA1-3 : bond 0.00107 ( 2) link_ALPHA1-3 : angle 1.53220 ( 6) link_ALPHA1-6 : bond 0.00595 ( 4) link_ALPHA1-6 : angle 2.47476 ( 12) link_BETA1-4 : bond 0.00359 ( 10) link_BETA1-4 : angle 2.61998 ( 30) link_NAG-ASN : bond 0.12660 ( 7) link_NAG-ASN : angle 7.54415 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6898 (mm-30) REVERT: D 242 MET cc_start: 0.7883 (tpt) cc_final: 0.7267 (tpt) REVERT: B 47 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7351 (mm-30) REVERT: F 184 ASP cc_start: 0.7278 (m-30) cc_final: 0.6614 (p0) REVERT: G 189 GLU cc_start: 0.7665 (tt0) cc_final: 0.7132 (tp30) outliers start: 10 outliers final: 4 residues processed: 272 average time/residue: 1.2825 time to fit residues: 402.9868 Evaluate side-chains 236 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain B residue 437 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS C 36 GLN C 208 GLN E 169 HIS E 430 HIS D 60 HIS D 70 ASN D 231 ASN B 272 GLN B 301 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111532 restraints weight = 71326.765| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.10 r_work: 0.3257 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20807 Z= 0.138 Angle : 0.589 10.248 28399 Z= 0.296 Chirality : 0.045 0.346 3321 Planarity : 0.005 0.154 3503 Dihedral : 10.666 115.644 3364 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.71 % Favored : 98.25 % Rotamer: Outliers : 1.56 % Allowed : 13.25 % Favored : 85.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.30 (0.17), residues: 2451 helix: 2.46 (0.18), residues: 802 sheet: 0.26 (0.20), residues: 594 loop : 0.05 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 301 TYR 0.014 0.001 TYR C 127 PHE 0.015 0.001 PHE C 256 TRP 0.015 0.001 TRP B 55 HIS 0.009 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00306 (20773) covalent geometry : angle 0.57303 (28310) SS BOND : bond 0.00661 ( 10) SS BOND : angle 2.52219 ( 20) hydrogen bonds : bond 0.04591 ( 1002) hydrogen bonds : angle 4.82304 ( 3159) Misc. bond : bond 0.00152 ( 1) link_ALPHA1-3 : bond 0.00931 ( 2) link_ALPHA1-3 : angle 2.10544 ( 6) link_ALPHA1-6 : bond 0.01338 ( 4) link_ALPHA1-6 : angle 2.05397 ( 12) link_BETA1-4 : bond 0.00426 ( 10) link_BETA1-4 : angle 2.29488 ( 30) link_NAG-ASN : bond 0.00397 ( 7) link_NAG-ASN : angle 3.14800 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6680 (tmt) REVERT: A 398 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7319 (mm-30) REVERT: A 420 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 386 MET cc_start: 0.7223 (mtp) cc_final: 0.6963 (mtp) REVERT: E 59 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8383 (mm-30) REVERT: D 186 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: D 436 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: F 184 ASP cc_start: 0.7804 (m-30) cc_final: 0.7473 (m-30) REVERT: G 189 GLU cc_start: 0.7864 (tt0) cc_final: 0.6940 (tp30) outliers start: 35 outliers final: 11 residues processed: 266 average time/residue: 1.1930 time to fit residues: 369.9875 Evaluate side-chains 238 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 132 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 0.0170 chunk 224 optimal weight: 0.8980 chunk 221 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN E 169 HIS E 315 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109398 restraints weight = 71582.208| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.97 r_work: 0.3226 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20807 Z= 0.150 Angle : 0.553 7.585 28399 Z= 0.277 Chirality : 0.045 0.361 3321 Planarity : 0.004 0.066 3503 Dihedral : 8.917 98.498 3359 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 2.01 % Allowed : 12.99 % Favored : 85.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.41 (0.17), residues: 2451 helix: 2.61 (0.18), residues: 801 sheet: 0.32 (0.20), residues: 612 loop : 0.05 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.013 0.001 TYR F 126 PHE 0.011 0.001 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.008 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00341 (20773) covalent geometry : angle 0.53991 (28310) SS BOND : bond 0.01073 ( 10) SS BOND : angle 1.78231 ( 20) hydrogen bonds : bond 0.04392 ( 1002) hydrogen bonds : angle 4.53684 ( 3159) Misc. bond : bond 0.00072 ( 1) link_ALPHA1-3 : bond 0.01100 ( 2) link_ALPHA1-3 : angle 1.65402 ( 6) link_ALPHA1-6 : bond 0.00684 ( 4) link_ALPHA1-6 : angle 1.67764 ( 12) link_BETA1-4 : bond 0.00450 ( 10) link_BETA1-4 : angle 2.36647 ( 30) link_NAG-ASN : bond 0.00401 ( 7) link_NAG-ASN : angle 2.67958 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6667 (tmt) REVERT: A 324 MET cc_start: 0.5116 (ttt) cc_final: 0.4112 (ttp) REVERT: C 384 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: E 59 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8396 (mm-30) REVERT: D 5 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: D 186 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: D 436 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: B 414 THR cc_start: 0.8706 (m) cc_final: 0.8372 (p) REVERT: F 184 ASP cc_start: 0.7802 (m-30) cc_final: 0.7489 (m-30) REVERT: G 63 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7667 (mtt180) REVERT: G 189 GLU cc_start: 0.7915 (tt0) cc_final: 0.6939 (tp30) outliers start: 45 outliers final: 14 residues processed: 263 average time/residue: 1.1936 time to fit residues: 367.2276 Evaluate side-chains 249 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 220 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS E 169 HIS E 308 ASN B 258 ASN B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106236 restraints weight = 72038.742| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.12 r_work: 0.3179 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20807 Z= 0.194 Angle : 0.563 7.694 28399 Z= 0.286 Chirality : 0.045 0.352 3321 Planarity : 0.005 0.055 3503 Dihedral : 8.508 93.064 3359 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 2.01 % Allowed : 13.48 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 1.35 (0.17), residues: 2451 helix: 2.50 (0.18), residues: 805 sheet: 0.31 (0.20), residues: 624 loop : 0.04 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.013 0.001 TYR A 198 PHE 0.015 0.002 PHE A 105 TRP 0.016 0.001 TRP B 55 HIS 0.008 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00450 (20773) covalent geometry : angle 0.55197 (28310) SS BOND : bond 0.00637 ( 10) SS BOND : angle 1.99958 ( 20) hydrogen bonds : bond 0.04474 ( 1002) hydrogen bonds : angle 4.50696 ( 3159) Misc. bond : bond 0.00060 ( 1) link_ALPHA1-3 : bond 0.01041 ( 2) link_ALPHA1-3 : angle 1.85393 ( 6) link_ALPHA1-6 : bond 0.00640 ( 4) link_ALPHA1-6 : angle 1.52459 ( 12) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 2.45697 ( 30) link_NAG-ASN : bond 0.00244 ( 7) link_NAG-ASN : angle 1.97296 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6711 (tmt) REVERT: A 324 MET cc_start: 0.5335 (ttt) cc_final: 0.4875 (ttp) REVERT: A 398 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7432 (mm-30) REVERT: C 384 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: E 59 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: D 186 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: D 436 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: B 26 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: B 251 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: F 32 GLN cc_start: 0.7255 (tt0) cc_final: 0.6937 (tm-30) REVERT: F 184 ASP cc_start: 0.7762 (m-30) cc_final: 0.7495 (m-30) REVERT: G 63 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7687 (mtt180) REVERT: G 94 ASP cc_start: 0.7653 (m-30) cc_final: 0.7417 (m-30) REVERT: G 189 GLU cc_start: 0.7985 (tt0) cc_final: 0.7007 (tp30) outliers start: 45 outliers final: 20 residues processed: 266 average time/residue: 1.2047 time to fit residues: 373.9323 Evaluate side-chains 248 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 158 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS C 393 ASN E 169 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107528 restraints weight = 72017.381| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.03 r_work: 0.3205 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20807 Z= 0.128 Angle : 0.515 7.191 28399 Z= 0.261 Chirality : 0.044 0.353 3321 Planarity : 0.004 0.053 3503 Dihedral : 8.089 84.955 3359 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 2.14 % Allowed : 13.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.44 (0.17), residues: 2451 helix: 2.61 (0.18), residues: 804 sheet: 0.31 (0.20), residues: 620 loop : 0.11 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.012 0.001 TYR F 126 PHE 0.012 0.001 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.006 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00288 (20773) covalent geometry : angle 0.50666 (28310) SS BOND : bond 0.00489 ( 10) SS BOND : angle 1.30452 ( 20) hydrogen bonds : bond 0.04125 ( 1002) hydrogen bonds : angle 4.38010 ( 3159) Misc. bond : bond 0.00031 ( 1) link_ALPHA1-3 : bond 0.00769 ( 2) link_ALPHA1-3 : angle 1.73705 ( 6) link_ALPHA1-6 : bond 0.00721 ( 4) link_ALPHA1-6 : angle 1.47106 ( 12) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 2.10269 ( 30) link_NAG-ASN : bond 0.00180 ( 7) link_NAG-ASN : angle 1.73255 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6713 (tmt) REVERT: A 324 MET cc_start: 0.5408 (ttt) cc_final: 0.4354 (ttp) REVERT: A 398 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7424 (mm-30) REVERT: E 59 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8365 (mm-30) REVERT: D 186 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: D 436 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: B 26 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: B 131 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: B 251 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: B 414 THR cc_start: 0.8752 (m) cc_final: 0.8419 (p) REVERT: F 32 GLN cc_start: 0.7317 (tt0) cc_final: 0.6991 (tm-30) REVERT: F 184 ASP cc_start: 0.7747 (m-30) cc_final: 0.7478 (m-30) REVERT: G 63 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7632 (mtt180) REVERT: G 189 GLU cc_start: 0.7982 (tt0) cc_final: 0.7008 (tp30) outliers start: 48 outliers final: 22 residues processed: 258 average time/residue: 1.1773 time to fit residues: 357.6324 Evaluate side-chains 256 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 33 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 169 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106217 restraints weight = 72512.355| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.10 r_work: 0.3181 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20807 Z= 0.176 Angle : 0.540 7.522 28399 Z= 0.273 Chirality : 0.044 0.350 3321 Planarity : 0.004 0.051 3503 Dihedral : 7.595 70.663 3359 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 2.05 % Allowed : 13.83 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.40 (0.17), residues: 2451 helix: 2.58 (0.18), residues: 803 sheet: 0.28 (0.20), residues: 622 loop : 0.09 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 429 TYR 0.012 0.001 TYR A 198 PHE 0.015 0.001 PHE C 284 TRP 0.017 0.001 TRP B 55 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00409 (20773) covalent geometry : angle 0.52946 (28310) SS BOND : bond 0.00513 ( 10) SS BOND : angle 1.51162 ( 20) hydrogen bonds : bond 0.04317 ( 1002) hydrogen bonds : angle 4.39762 ( 3159) Misc. bond : bond 0.00051 ( 1) link_ALPHA1-3 : bond 0.01059 ( 2) link_ALPHA1-3 : angle 1.82861 ( 6) link_ALPHA1-6 : bond 0.00853 ( 4) link_ALPHA1-6 : angle 1.62427 ( 12) link_BETA1-4 : bond 0.00397 ( 10) link_BETA1-4 : angle 2.31593 ( 30) link_NAG-ASN : bond 0.00143 ( 7) link_NAG-ASN : angle 1.88554 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6721 (tmt) REVERT: A 324 MET cc_start: 0.5359 (ttt) cc_final: 0.4428 (ttp) REVERT: A 398 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7437 (mm-30) REVERT: E 59 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: D 186 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: D 436 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: B 71 ASP cc_start: 0.7921 (t0) cc_final: 0.7707 (t0) REVERT: B 131 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: F 32 GLN cc_start: 0.7375 (tt0) cc_final: 0.7049 (tm-30) REVERT: F 184 ASP cc_start: 0.7764 (m-30) cc_final: 0.7502 (m-30) REVERT: G 63 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7663 (mtt180) REVERT: G 189 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7008 (tp30) outliers start: 46 outliers final: 24 residues processed: 258 average time/residue: 1.1503 time to fit residues: 350.0489 Evaluate side-chains 256 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 189 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 109 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS C 393 ASN E 169 HIS B 251 GLN B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107095 restraints weight = 71866.387| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.02 r_work: 0.3196 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20807 Z= 0.144 Angle : 0.520 7.140 28399 Z= 0.262 Chirality : 0.044 0.353 3321 Planarity : 0.004 0.050 3503 Dihedral : 7.289 71.793 3359 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 1.87 % Allowed : 14.15 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.49 (0.17), residues: 2451 helix: 2.66 (0.18), residues: 801 sheet: 0.32 (0.20), residues: 621 loop : 0.16 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.012 0.001 TYR F 126 PHE 0.012 0.001 PHE C 284 TRP 0.017 0.001 TRP B 55 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00331 (20773) covalent geometry : angle 0.51066 (28310) SS BOND : bond 0.00481 ( 10) SS BOND : angle 1.29255 ( 20) hydrogen bonds : bond 0.04157 ( 1002) hydrogen bonds : angle 4.33035 ( 3159) Misc. bond : bond 0.00035 ( 1) link_ALPHA1-3 : bond 0.00964 ( 2) link_ALPHA1-3 : angle 1.87104 ( 6) link_ALPHA1-6 : bond 0.00913 ( 4) link_ALPHA1-6 : angle 1.73836 ( 12) link_BETA1-4 : bond 0.00359 ( 10) link_BETA1-4 : angle 2.11644 ( 30) link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.65015 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6715 (tmt) REVERT: A 324 MET cc_start: 0.5206 (ttt) cc_final: 0.4224 (ttp) REVERT: A 398 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7429 (mm-30) REVERT: E 59 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: D 186 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: D 436 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: B 71 ASP cc_start: 0.7903 (t0) cc_final: 0.7683 (t0) REVERT: B 131 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: F 32 GLN cc_start: 0.7340 (tt0) cc_final: 0.7028 (tm-30) REVERT: F 184 ASP cc_start: 0.7776 (m-30) cc_final: 0.7526 (m-30) REVERT: G 63 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (mtt180) REVERT: G 189 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6998 (tp30) outliers start: 42 outliers final: 25 residues processed: 255 average time/residue: 1.1414 time to fit residues: 342.2821 Evaluate side-chains 255 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 189 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 23 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 137 optimal weight: 0.0270 chunk 46 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 169 HIS D 97 ASN B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105854 restraints weight = 72248.384| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.10 r_work: 0.3175 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20807 Z= 0.162 Angle : 0.529 7.452 28399 Z= 0.268 Chirality : 0.044 0.348 3321 Planarity : 0.004 0.050 3503 Dihedral : 7.218 76.587 3359 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 1.70 % Allowed : 14.73 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.48 (0.17), residues: 2451 helix: 2.64 (0.18), residues: 801 sheet: 0.31 (0.20), residues: 623 loop : 0.16 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 429 TYR 0.011 0.001 TYR F 126 PHE 0.014 0.001 PHE C 284 TRP 0.017 0.001 TRP B 55 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00376 (20773) covalent geometry : angle 0.52019 (28310) SS BOND : bond 0.00480 ( 10) SS BOND : angle 1.38268 ( 20) hydrogen bonds : bond 0.04230 ( 1002) hydrogen bonds : angle 4.33821 ( 3159) Misc. bond : bond 0.00043 ( 1) link_ALPHA1-3 : bond 0.00927 ( 2) link_ALPHA1-3 : angle 1.74201 ( 6) link_ALPHA1-6 : bond 0.00863 ( 4) link_ALPHA1-6 : angle 1.72647 ( 12) link_BETA1-4 : bond 0.00374 ( 10) link_BETA1-4 : angle 2.15569 ( 30) link_NAG-ASN : bond 0.00124 ( 7) link_NAG-ASN : angle 1.80014 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6730 (tmt) REVERT: A 398 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7524 (mm-30) REVERT: E 59 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8396 (mm-30) REVERT: D 186 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: D 436 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 71 ASP cc_start: 0.7941 (t0) cc_final: 0.7689 (t0) REVERT: B 131 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: F 32 GLN cc_start: 0.7361 (tt0) cc_final: 0.7057 (tm-30) REVERT: F 184 ASP cc_start: 0.7796 (m-30) cc_final: 0.7536 (m-30) REVERT: G 189 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7022 (tp30) outliers start: 38 outliers final: 24 residues processed: 254 average time/residue: 1.1678 time to fit residues: 350.1361 Evaluate side-chains 257 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 189 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS C 393 ASN E 169 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105371 restraints weight = 72250.348| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.07 r_work: 0.3169 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20807 Z= 0.181 Angle : 0.541 8.102 28399 Z= 0.274 Chirality : 0.044 0.355 3321 Planarity : 0.004 0.050 3503 Dihedral : 7.249 80.194 3359 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 1.74 % Allowed : 14.95 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.44 (0.17), residues: 2451 helix: 2.60 (0.18), residues: 802 sheet: 0.31 (0.20), residues: 623 loop : 0.13 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 63 TYR 0.011 0.001 TYR A 198 PHE 0.014 0.001 PHE C 284 TRP 0.028 0.001 TRP G 172 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00422 (20773) covalent geometry : angle 0.53197 (28310) SS BOND : bond 0.00521 ( 10) SS BOND : angle 1.49610 ( 20) hydrogen bonds : bond 0.04342 ( 1002) hydrogen bonds : angle 4.36078 ( 3159) Misc. bond : bond 0.00050 ( 1) link_ALPHA1-3 : bond 0.00988 ( 2) link_ALPHA1-3 : angle 1.77089 ( 6) link_ALPHA1-6 : bond 0.00848 ( 4) link_ALPHA1-6 : angle 1.70125 ( 12) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 2.18550 ( 30) link_NAG-ASN : bond 0.00092 ( 7) link_NAG-ASN : angle 1.71268 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6681 (tmt) REVERT: A 324 MET cc_start: 0.6221 (ttm) cc_final: 0.5486 (ttp) REVERT: A 398 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7482 (mm-30) REVERT: E 59 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8361 (mm-30) REVERT: D 182 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: D 186 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: D 436 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: B 71 ASP cc_start: 0.7989 (t0) cc_final: 0.7717 (t0) REVERT: B 131 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: F 32 GLN cc_start: 0.7423 (tt0) cc_final: 0.7091 (tm-30) REVERT: F 184 ASP cc_start: 0.7831 (m-30) cc_final: 0.7566 (m-30) REVERT: G 189 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7005 (tp30) outliers start: 39 outliers final: 26 residues processed: 252 average time/residue: 1.1680 time to fit residues: 347.3839 Evaluate side-chains 253 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 208 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 142 optimal weight: 0.0980 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 169 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108031 restraints weight = 71963.295| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3205 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20807 Z= 0.104 Angle : 0.499 8.103 28399 Z= 0.253 Chirality : 0.043 0.344 3321 Planarity : 0.004 0.052 3503 Dihedral : 6.879 80.569 3359 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 15.08 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.60 (0.17), residues: 2451 helix: 2.74 (0.18), residues: 803 sheet: 0.30 (0.20), residues: 619 loop : 0.28 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 63 TYR 0.013 0.001 TYR F 126 PHE 0.013 0.001 PHE C 256 TRP 0.022 0.001 TRP F 194 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00230 (20773) covalent geometry : angle 0.49099 (28310) SS BOND : bond 0.00422 ( 10) SS BOND : angle 1.10644 ( 20) hydrogen bonds : bond 0.03929 ( 1002) hydrogen bonds : angle 4.22393 ( 3159) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-3 : bond 0.00813 ( 2) link_ALPHA1-3 : angle 1.77647 ( 6) link_ALPHA1-6 : bond 0.00848 ( 4) link_ALPHA1-6 : angle 1.67944 ( 12) link_BETA1-4 : bond 0.00373 ( 10) link_BETA1-4 : angle 1.84703 ( 30) link_NAG-ASN : bond 0.00233 ( 7) link_NAG-ASN : angle 1.62583 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6709 (tmt) REVERT: A 324 MET cc_start: 0.6181 (ttm) cc_final: 0.5404 (ttp) REVERT: A 398 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7502 (mm-30) REVERT: E 59 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: D 186 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: D 436 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: B 71 ASP cc_start: 0.8003 (t0) cc_final: 0.7715 (t0) REVERT: B 131 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: F 32 GLN cc_start: 0.7444 (tt0) cc_final: 0.7129 (tm-30) REVERT: F 184 ASP cc_start: 0.7764 (m-30) cc_final: 0.7521 (m-30) REVERT: G 189 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7014 (tp30) outliers start: 29 outliers final: 18 residues processed: 246 average time/residue: 1.2045 time to fit residues: 347.3265 Evaluate side-chains 248 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 1 LYS Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 169 HIS B 272 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106927 restraints weight = 72615.615| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.05 r_work: 0.3191 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20807 Z= 0.136 Angle : 0.510 8.481 28399 Z= 0.258 Chirality : 0.043 0.349 3321 Planarity : 0.004 0.052 3503 Dihedral : 6.856 81.568 3359 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.25 % Allowed : 15.22 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.80 % 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 aren not related in a simple way. whole: 1.59 (0.17), residues: 2451 helix: 2.73 (0.18), residues: 803 sheet: 0.34 (0.20), residues: 621 loop : 0.25 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 429 TYR 0.012 0.001 TYR F 126 PHE 0.013 0.001 PHE C 284 TRP 0.028 0.001 TRP F 194 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00316 (20773) covalent geometry : angle 0.50148 (28310) SS BOND : bond 0.00447 ( 10) SS BOND : angle 1.30007 ( 20) hydrogen bonds : bond 0.04054 ( 1002) hydrogen bonds : angle 4.23183 ( 3159) Misc. bond : bond 0.00031 ( 1) link_ALPHA1-3 : bond 0.00892 ( 2) link_ALPHA1-3 : angle 1.68232 ( 6) link_ALPHA1-6 : bond 0.00839 ( 4) link_ALPHA1-6 : angle 1.64490 ( 12) link_BETA1-4 : bond 0.00352 ( 10) link_BETA1-4 : angle 1.99024 ( 30) link_NAG-ASN : bond 0.00113 ( 7) link_NAG-ASN : angle 1.65249 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15914.71 seconds wall clock time: 270 minutes 8.14 seconds (16208.14 seconds total)