Starting phenix.real_space_refine on Tue Aug 26 20:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmv_47017/08_2025/9dmv_47017_neut_trim.cif" } resolution = 2.13 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= 0.027 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 4 5.49 5 S 85 5.16 5 C 13284 2.51 5 N 3260 2.21 5 O 3791 1.98 5 H 19779 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 40203 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6411 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 377} 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: 6551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6551 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 378} Chain breaks: 3 Chain: "D" Number of atoms: 7053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7053 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: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3339 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain breaks: 1 Chain: "G" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3205 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 198} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'CLR': 3, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 100 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 6.00, per 1000 atoms: 0.15 Number of scatterers: 40203 At special positions: 0 Unit cell: (109.395, 143.99, 214.115, 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 85 16.00 P 4 15.00 O 3791 8.00 N 3260 7.00 C 13284 6.00 H 19779 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=2.05 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 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 128 " distance=2.04 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " 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 M 1 " - " NAG M 2 " NAG-ASN " NAG D 501 " - " ASN D 76 " " 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 " " NAG M 1 " - " ASN B 66 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4718 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 30 sheets defined 38.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.986A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.503A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.968A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.594A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (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: 4.169A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 324' Processing helix chain 'A' and resid 370 through 437 removed outlier: 3.692A pdb=" N THR A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.475A 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: 4.033A 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: 3.870A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.862A 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 236 through 240 Processing helix chain 'C' and resid 241 through 264 removed outlier: 4.082A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.083A 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 318 removed outlier: 3.563A pdb=" N ASP C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 369 through 435 removed outlier: 3.530A pdb=" N PHE C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.203A 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 273 removed outlier: 4.124A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 328 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.981A 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 65 through 68 removed outlier: 3.508A pdb=" N LYS D 68 " --> pdb=" O ASN D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 70 through 75 removed outlier: 4.061A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) 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 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.557A pdb=" N VAL D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 3.949A 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 removed outlier: 3.675A pdb=" N GLU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 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: 3.753A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.823A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.088A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) 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 237 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.886A 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 328 removed outlier: 3.524A pdb=" N ARG B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.066A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.729A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 229 through 232 removed outlier: 4.165A pdb=" N GLY F 232 " --> pdb=" O SER F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 243 through 246 Processing helix chain 'G' and resid 98 through 102 removed outlier: 4.032A pdb=" N PHE G 102 " --> pdb=" O PRO G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 202 through 206 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.957A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.957A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N VAL A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N THR A 32 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.738A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.490A 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: 4.247A 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: 4.247A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL C 29 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 31 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.780A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR C 196 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 190 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 180 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.558A 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: 4.107A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.651A 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: 4.107A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.340A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.889A 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: 3.890A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.890A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.155A 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: 6.869A 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 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.641A 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: 3.641A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 43 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 51 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU B 37 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 57 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 35 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP B 59 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 33 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLN B 61 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 31 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.133A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.716A 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: 5.133A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.546A 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 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 removed outlier: 7.803A pdb=" N TYR F 65 " --> pdb=" O TYR F 85 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR F 85 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP F 67 " --> pdb=" O HIS F 83 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS F 83 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 69 " --> pdb=" O ILE F 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.799A pdb=" N CYS F 128 " --> pdb=" O TRP F 145 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP F 145 " --> pdb=" O CYS F 128 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG F 130 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 162 through 166 removed outlier: 5.069A pdb=" N ALA F 179 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 226 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY F 181 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 224 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU F 183 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER F 222 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS F 185 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 220 " --> pdb=" O LYS F 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 162 through 166 removed outlier: 5.069A pdb=" N ALA F 179 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 226 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY F 181 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 224 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU F 183 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER F 222 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS F 185 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 220 " --> pdb=" O LYS F 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 193 through 196 removed outlier: 4.358A pdb=" N TYR F 236 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 26 removed outlier: 3.747A pdb=" N TYR G 90 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.555A pdb=" N LEU G 52 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR G 68 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP G 54 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.734A pdb=" N ILE G 116 " --> pdb=" O GLN G 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 133 through 137 removed outlier: 5.800A pdb=" N TYR G 192 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 172 through 173 1122 hydrogen bonds defined for protein. 3123 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: 10.55 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19760 1.03 - 1.23: 253 1.23 - 1.43: 8360 1.43 - 1.62: 12215 1.62 - 1.82: 131 Bond restraints: 40719 Sorted by residual: bond pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" N VAL C 22 " pdb=" CA VAL C 22 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.11e-02 8.12e+03 1.65e+01 bond pdb=" NZ LYS E 274 " pdb=" HZ3 LYS E 274 " 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 G 209 " pdb=" HZ1 LYS G 209 " 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 328 " pdb=" HZ3 LYS D 328 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 40714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.26: 73474 12.26 - 24.52: 2 24.52 - 36.78: 0 36.78 - 49.04: 3 49.04 - 61.30: 3 Bond angle restraints: 73482 Sorted by residual: angle pdb=" CA LEU C 366 " pdb=" N LEU C 366 " pdb=" H LEU C 366 " ideal model delta sigma weight residual 114.00 175.30 -61.30 3.00e+00 1.11e-01 4.17e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 172.11 -58.11 3.00e+00 1.11e-01 3.75e+02 angle pdb=" CA ALA B 397 " pdb=" N ALA B 397 " pdb=" H ALA B 397 " ideal model delta sigma weight residual 114.00 169.77 -55.77 3.00e+00 1.11e-01 3.46e+02 angle pdb=" CA GLN D 408 " pdb=" N GLN D 408 " pdb=" H GLN D 408 " ideal model delta sigma weight residual 114.00 160.06 -46.06 3.00e+00 1.11e-01 2.36e+02 angle pdb=" CA GLY F 176 " pdb=" N GLY F 176 " pdb=" H GLY F 176 " ideal model delta sigma weight residual 114.00 155.53 -41.53 3.00e+00 1.11e-01 1.92e+02 ... (remaining 73477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 19361 34.46 - 68.92: 556 68.92 - 103.39: 80 103.39 - 137.85: 17 137.85 - 172.31: 1 Dihedral angle restraints: 20015 sinusoidal: 11295 harmonic: 8720 Sorted by residual: dihedral pdb=" CB CYS F 53 " pdb=" SG CYS F 53 " pdb=" SG CYS F 128 " pdb=" CB CYS F 128 " ideal model delta sinusoidal sigma weight residual 93.00 49.82 43.18 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CD ARG G 127 " pdb=" NE ARG G 127 " pdb=" CZ ARG G 127 " pdb=" NH1 ARG G 127 " ideal model delta sinusoidal sigma weight residual 0.00 -39.23 39.23 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" C27 POV A 501 " pdb=" C28 POV A 501 " pdb=" C29 POV A 501 " pdb="C210 POV A 501 " ideal model delta sinusoidal sigma weight residual 127.48 -60.21 -172.31 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 20012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3062 0.087 - 0.174: 314 0.174 - 0.261: 12 0.261 - 0.348: 2 0.348 - 0.435: 1 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.11e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.37e+01 chirality pdb=" C1 MAN K 5 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 5 " pdb=" O5 MAN K 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.27e+01 ... (remaining 3388 not shown) Planarity restraints: 5816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 503 " -0.065 2.00e-02 2.50e+03 2.57e-01 6.59e+02 pdb=" C29 POV D 503 " 0.307 2.00e-02 2.50e+03 pdb="C210 POV D 503 " -0.381 2.00e-02 2.50e+03 pdb="C211 POV D 503 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.213 2.00e-02 2.50e+03 1.80e-01 4.04e+02 pdb=" C7 NAG M 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.302 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 9 " 0.551 9.50e-02 1.11e+02 2.21e-01 3.72e+02 pdb=" NE ARG D 9 " 0.095 2.00e-02 2.50e+03 pdb=" CZ ARG D 9 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG D 9 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 9 " -0.025 2.00e-02 2.50e+03 pdb="HH11 ARG D 9 " -0.259 2.00e-02 2.50e+03 pdb="HH12 ARG D 9 " 0.227 2.00e-02 2.50e+03 pdb="HH21 ARG D 9 " -0.061 2.00e-02 2.50e+03 pdb="HH22 ARG D 9 " -0.045 2.00e-02 2.50e+03 ... (remaining 5813 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 535 2.09 - 2.72: 66694 2.72 - 3.35: 115690 3.35 - 3.97: 157333 3.97 - 4.60: 239521 Nonbonded interactions: 579773 Sorted by model distance: nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.464 2.100 nonbonded pdb=" HH TYR C 381 " pdb="HD21 ASN D 432 " model vdw 1.477 2.100 nonbonded pdb=" HE1 HIS A 306 " pdb=" O13 POV B 503 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.632 2.100 nonbonded pdb=" OE2 GLU B 89 " pdb=" HG1 THR B 150 " model vdw 1.658 2.450 ... (remaining 579768 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 329 or resid 369 through 436)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.420 Find NCS groups from input model: 0.300 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.770 20978 Z= 0.614 Angle : 0.861 13.135 28666 Z= 0.457 Chirality : 0.052 0.435 3391 Planarity : 0.012 0.293 3492 Dihedral : 17.027 172.308 8384 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 0.31 % Allowed : 10.37 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.13 (0.17), residues: 2445 helix: 2.21 (0.18), residues: 803 sheet: 0.27 (0.20), residues: 625 loop : -0.04 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 443 TYR 0.018 0.001 TYR A 381 PHE 0.022 0.002 PHE G 137 TRP 0.015 0.001 TRP B 55 HIS 0.021 0.002 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00540 (20940) covalent geometry : angle 0.83082 (28565) SS BOND : bond 0.01189 ( 10) SS BOND : angle 1.65240 ( 20) hydrogen bonds : bond 0.12554 ( 1018) hydrogen bonds : angle 5.52435 ( 3123) Misc. bond : bond 0.76995 ( 1) link_ALPHA1-3 : bond 0.00137 ( 5) link_ALPHA1-3 : angle 1.43938 ( 15) link_ALPHA1-6 : bond 0.00139 ( 4) link_ALPHA1-6 : angle 1.12697 ( 12) link_BETA1-4 : bond 0.00696 ( 11) link_BETA1-4 : angle 2.20532 ( 33) link_NAG-ASN : bond 0.14006 ( 7) link_NAG-ASN : angle 7.76709 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: C 306 HIS cc_start: 0.6868 (m90) cc_final: 0.6421 (m90) REVERT: C 329 MET cc_start: 0.7103 (mtt) cc_final: 0.6517 (mtp) REVERT: E 452 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: D 5 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 316 HIS cc_start: 0.6493 (m-70) cc_final: 0.6226 (m90) REVERT: F 138 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8026 (mtp85) outliers start: 7 outliers final: 2 residues processed: 239 average time/residue: 1.2682 time to fit residues: 341.4142 Evaluate side-chains 221 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 186 HIS A 204 HIS A 297 ASN A 322 ASN C 393 ASN E 131 GLN D 475 GLN F 147 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108648 restraints weight = 58259.254| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.04 r_work: 0.3192 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20978 Z= 0.145 Angle : 0.583 7.876 28666 Z= 0.292 Chirality : 0.044 0.281 3391 Planarity : 0.005 0.065 3492 Dihedral : 12.010 157.658 3722 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 0.71 % Allowed : 10.10 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.41 (0.17), residues: 2445 helix: 2.48 (0.18), residues: 810 sheet: 0.43 (0.20), residues: 622 loop : 0.07 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 443 TYR 0.012 0.001 TYR D 119 PHE 0.017 0.002 PHE F 111 TRP 0.011 0.001 TRP B 55 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00310 (20940) covalent geometry : angle 0.57167 (28565) SS BOND : bond 0.00413 ( 10) SS BOND : angle 1.05262 ( 20) hydrogen bonds : bond 0.05152 ( 1018) hydrogen bonds : angle 4.64163 ( 3123) Misc. bond : bond 0.00405 ( 1) link_ALPHA1-3 : bond 0.00793 ( 5) link_ALPHA1-3 : angle 2.34496 ( 15) link_ALPHA1-6 : bond 0.00629 ( 4) link_ALPHA1-6 : angle 1.84918 ( 12) link_BETA1-4 : bond 0.00354 ( 11) link_BETA1-4 : angle 2.13285 ( 33) link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 2.28564 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 1.042 Fit side-chains REVERT: C 2 GLU cc_start: 0.6781 (tp30) cc_final: 0.6539 (tp30) REVERT: C 129 GLU cc_start: 0.8181 (tt0) cc_final: 0.7960 (tt0) REVERT: C 329 MET cc_start: 0.7093 (mtt) cc_final: 0.6479 (mtp) REVERT: C 398 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 6 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8361 (mtm110) REVERT: E 452 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: D 5 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 198 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6744 (t-90) REVERT: F 96 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7326 (mt) REVERT: F 138 ARG cc_start: 0.8443 (mtm110) cc_final: 0.7684 (mtp85) REVERT: G 124 GLU cc_start: 0.7238 (pm20) cc_final: 0.6823 (pp20) outliers start: 16 outliers final: 2 residues processed: 244 average time/residue: 1.1881 time to fit residues: 327.8543 Evaluate side-chains 226 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 221 optimal weight: 10.0000 chunk 211 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 239 optimal weight: 30.0000 chunk 218 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN C 111 GLN C 186 HIS C 393 ASN E 131 GLN D 475 GLN B 316 HIS F 147 GLN G 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104665 restraints weight = 57807.878| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.59 r_work: 0.3147 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20978 Z= 0.198 Angle : 0.598 8.971 28666 Z= 0.306 Chirality : 0.045 0.207 3391 Planarity : 0.005 0.067 3492 Dihedral : 10.909 135.466 3720 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 0.89 % Allowed : 10.15 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.39 (0.17), residues: 2445 helix: 2.39 (0.17), residues: 812 sheet: 0.43 (0.20), residues: 636 loop : 0.11 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 127 TYR 0.013 0.002 TYR C 198 PHE 0.020 0.002 PHE C 284 TRP 0.019 0.002 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00438 (20940) covalent geometry : angle 0.58711 (28565) SS BOND : bond 0.00536 ( 10) SS BOND : angle 1.38342 ( 20) hydrogen bonds : bond 0.05571 ( 1018) hydrogen bonds : angle 4.64732 ( 3123) Misc. bond : bond 0.00180 ( 1) link_ALPHA1-3 : bond 0.01043 ( 5) link_ALPHA1-3 : angle 1.77319 ( 15) link_ALPHA1-6 : bond 0.00705 ( 4) link_ALPHA1-6 : angle 1.63602 ( 12) link_BETA1-4 : bond 0.00529 ( 11) link_BETA1-4 : angle 2.39445 ( 33) link_NAG-ASN : bond 0.00469 ( 7) link_NAG-ASN : angle 2.21654 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.860 Fit side-chains REVERT: C 398 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7781 (mt-10) REVERT: E 6 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8399 (mtm110) REVERT: E 152 ASP cc_start: 0.8611 (p0) cc_final: 0.8388 (p0) REVERT: E 452 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: D 5 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 86 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (mtp) REVERT: D 167 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6883 (tttm) REVERT: B 272 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6493 (mp10) REVERT: B 316 HIS cc_start: 0.6968 (m90) cc_final: 0.6447 (m90) REVERT: F 34 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7743 (mm-40) REVERT: G 124 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7064 (pp20) outliers start: 20 outliers final: 4 residues processed: 240 average time/residue: 1.1747 time to fit residues: 320.0241 Evaluate side-chains 228 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 150 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 230 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 39 GLN E 131 GLN D 475 GLN F 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104723 restraints weight = 57930.583| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20978 Z= 0.171 Angle : 0.565 9.154 28666 Z= 0.289 Chirality : 0.044 0.202 3391 Planarity : 0.005 0.057 3492 Dihedral : 10.167 111.852 3720 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 0.76 % Allowed : 10.19 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.42 (0.17), residues: 2445 helix: 2.46 (0.17), residues: 812 sheet: 0.50 (0.20), residues: 625 loop : 0.04 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.013 0.001 TYR E 225 PHE 0.018 0.002 PHE C 284 TRP 0.015 0.002 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00378 (20940) covalent geometry : angle 0.55177 (28565) SS BOND : bond 0.00417 ( 10) SS BOND : angle 1.18415 ( 20) hydrogen bonds : bond 0.05262 ( 1018) hydrogen bonds : angle 4.56056 ( 3123) Misc. bond : bond 0.00112 ( 1) link_ALPHA1-3 : bond 0.01039 ( 5) link_ALPHA1-3 : angle 1.95646 ( 15) link_ALPHA1-6 : bond 0.00814 ( 4) link_ALPHA1-6 : angle 1.69145 ( 12) link_BETA1-4 : bond 0.00436 ( 11) link_BETA1-4 : angle 2.24578 ( 33) link_NAG-ASN : bond 0.00383 ( 7) link_NAG-ASN : angle 2.82501 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 398 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7742 (mt-10) REVERT: E 6 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8391 (mtm110) REVERT: E 24 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7806 (mm-30) REVERT: E 152 ASP cc_start: 0.8546 (p0) cc_final: 0.8319 (p0) REVERT: E 452 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: D 86 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: D 167 LYS cc_start: 0.7177 (ttmm) cc_final: 0.6917 (tttm) REVERT: D 186 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: F 242 HIS cc_start: 0.5267 (t-90) cc_final: 0.5031 (t-90) outliers start: 17 outliers final: 2 residues processed: 232 average time/residue: 1.1410 time to fit residues: 301.0095 Evaluate side-chains 229 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 135 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 233 optimal weight: 0.5980 chunk 201 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN D 60 HIS D 475 GLN F 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107638 restraints weight = 58151.143| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.61 r_work: 0.3194 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20978 Z= 0.101 Angle : 0.499 7.105 28666 Z= 0.254 Chirality : 0.043 0.218 3391 Planarity : 0.004 0.046 3492 Dihedral : 8.967 89.531 3720 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 0.67 % Allowed : 10.24 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.62 (0.17), residues: 2445 helix: 2.71 (0.18), residues: 811 sheet: 0.57 (0.20), residues: 627 loop : 0.12 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 140 TYR 0.011 0.001 TYR F 187 PHE 0.017 0.001 PHE C 284 TRP 0.011 0.001 TRP B 55 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00209 (20940) covalent geometry : angle 0.48720 (28565) SS BOND : bond 0.00183 ( 10) SS BOND : angle 0.60348 ( 20) hydrogen bonds : bond 0.04455 ( 1018) hydrogen bonds : angle 4.31711 ( 3123) Misc. bond : bond 0.00081 ( 1) link_ALPHA1-3 : bond 0.00959 ( 5) link_ALPHA1-3 : angle 1.89163 ( 15) link_ALPHA1-6 : bond 0.01135 ( 4) link_ALPHA1-6 : angle 1.89138 ( 12) link_BETA1-4 : bond 0.00341 ( 11) link_BETA1-4 : angle 1.84060 ( 33) link_NAG-ASN : bond 0.00262 ( 7) link_NAG-ASN : angle 2.56137 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: C 329 MET cc_start: 0.7115 (mtt) cc_final: 0.6757 (mtp) REVERT: C 398 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 24 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7762 (mm-30) REVERT: E 313 SER cc_start: 0.8431 (m) cc_final: 0.8172 (p) REVERT: E 452 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: D 167 LYS cc_start: 0.7125 (ttmm) cc_final: 0.6884 (tttm) REVERT: D 186 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: F 96 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7277 (mt) REVERT: F 242 HIS cc_start: 0.5430 (t-90) cc_final: 0.5206 (t-170) outliers start: 15 outliers final: 4 residues processed: 242 average time/residue: 1.1255 time to fit residues: 309.3017 Evaluate side-chains 226 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 150 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN D 475 GLN F 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106844 restraints weight = 58466.679| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.63 r_work: 0.3180 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20978 Z= 0.121 Angle : 0.514 9.876 28666 Z= 0.261 Chirality : 0.043 0.205 3391 Planarity : 0.004 0.045 3492 Dihedral : 8.353 83.226 3720 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 0.62 % Allowed : 10.41 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.68 (0.17), residues: 2445 helix: 2.75 (0.18), residues: 812 sheet: 0.59 (0.20), residues: 630 loop : 0.16 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 20 TYR 0.010 0.001 TYR E 225 PHE 0.018 0.001 PHE C 284 TRP 0.010 0.001 TRP D 176 HIS 0.009 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00259 (20940) covalent geometry : angle 0.49690 (28565) SS BOND : bond 0.00281 ( 10) SS BOND : angle 0.86041 ( 20) hydrogen bonds : bond 0.04560 ( 1018) hydrogen bonds : angle 4.28669 ( 3123) Misc. bond : bond 0.00079 ( 1) link_ALPHA1-3 : bond 0.00913 ( 5) link_ALPHA1-3 : angle 1.67687 ( 15) link_ALPHA1-6 : bond 0.01116 ( 4) link_ALPHA1-6 : angle 2.35805 ( 12) link_BETA1-4 : bond 0.00324 ( 11) link_BETA1-4 : angle 2.00466 ( 33) link_NAG-ASN : bond 0.00227 ( 7) link_NAG-ASN : angle 3.52957 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: C 329 MET cc_start: 0.7130 (mtt) cc_final: 0.6770 (mtp) REVERT: C 398 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7730 (mt-10) REVERT: E 6 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8416 (mtm110) REVERT: E 24 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 313 SER cc_start: 0.8405 (m) cc_final: 0.8163 (p) REVERT: E 452 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: D 167 LYS cc_start: 0.7149 (ttmm) cc_final: 0.6914 (tttm) REVERT: D 186 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: D 334 LEU cc_start: 0.8266 (mt) cc_final: 0.8008 (mp) REVERT: B 272 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6434 (mp10) REVERT: F 154 SER cc_start: 0.6585 (m) cc_final: 0.6221 (p) REVERT: F 242 HIS cc_start: 0.5450 (t-90) cc_final: 0.5215 (t-170) outliers start: 14 outliers final: 3 residues processed: 232 average time/residue: 1.1864 time to fit residues: 311.9949 Evaluate side-chains 225 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 223 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 160 optimal weight: 0.3980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN E 325 GLN D 97 ASN D 475 GLN F 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105060 restraints weight = 58142.192| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.99 r_work: 0.3137 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20978 Z= 0.182 Angle : 0.570 13.880 28666 Z= 0.291 Chirality : 0.044 0.348 3391 Planarity : 0.005 0.060 3492 Dihedral : 8.592 90.082 3720 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.21 % Favored : 97.75 % Rotamer: Outliers : 0.85 % Allowed : 10.55 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.57 (0.17), residues: 2445 helix: 2.60 (0.17), residues: 812 sheet: 0.54 (0.20), residues: 637 loop : 0.13 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 209 TYR 0.012 0.002 TYR E 225 PHE 0.022 0.002 PHE C 284 TRP 0.017 0.002 TRP D 176 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00408 (20940) covalent geometry : angle 0.54724 (28565) SS BOND : bond 0.00475 ( 10) SS BOND : angle 1.32812 ( 20) hydrogen bonds : bond 0.05156 ( 1018) hydrogen bonds : angle 4.44092 ( 3123) Misc. bond : bond 0.00086 ( 1) link_ALPHA1-3 : bond 0.00883 ( 5) link_ALPHA1-3 : angle 1.66957 ( 15) link_ALPHA1-6 : bond 0.01092 ( 4) link_ALPHA1-6 : angle 2.11980 ( 12) link_BETA1-4 : bond 0.00424 ( 11) link_BETA1-4 : angle 2.25080 ( 33) link_NAG-ASN : bond 0.00577 ( 7) link_NAG-ASN : angle 4.69092 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: C 329 MET cc_start: 0.7149 (mtt) cc_final: 0.6786 (mtp) REVERT: C 398 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7787 (mt-10) REVERT: E 6 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8430 (mtm110) REVERT: E 24 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7867 (mm-30) REVERT: E 313 SER cc_start: 0.8433 (m) cc_final: 0.8194 (p) REVERT: E 318 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6420 (tm130) REVERT: E 452 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: D 86 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8516 (mtp) REVERT: D 167 LYS cc_start: 0.7227 (ttmm) cc_final: 0.7020 (tttm) REVERT: D 186 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: D 334 LEU cc_start: 0.8321 (mt) cc_final: 0.8060 (mp) REVERT: B 268 PHE cc_start: 0.8655 (t80) cc_final: 0.7958 (t80) REVERT: B 272 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6389 (mp10) REVERT: F 154 SER cc_start: 0.6556 (m) cc_final: 0.6182 (p) REVERT: F 242 HIS cc_start: 0.5417 (t-90) cc_final: 0.5215 (t-170) outliers start: 19 outliers final: 5 residues processed: 237 average time/residue: 1.2253 time to fit residues: 328.1668 Evaluate side-chains 234 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain E residue 318 GLN Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain G residue 150 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 198 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN D 475 GLN F 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105107 restraints weight = 57855.631| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.61 r_work: 0.3156 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20978 Z= 0.159 Angle : 0.556 14.274 28666 Z= 0.285 Chirality : 0.044 0.443 3391 Planarity : 0.004 0.054 3492 Dihedral : 8.381 90.000 3720 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 0.49 % Allowed : 11.13 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.55 (0.17), residues: 2445 helix: 2.59 (0.17), residues: 812 sheet: 0.54 (0.20), residues: 633 loop : 0.11 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.015 0.001 TYR E 225 PHE 0.021 0.002 PHE C 284 TRP 0.014 0.001 TRP D 176 HIS 0.009 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00348 (20940) covalent geometry : angle 0.53351 (28565) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.08927 ( 20) hydrogen bonds : bond 0.05016 ( 1018) hydrogen bonds : angle 4.42380 ( 3123) Misc. bond : bond 0.00073 ( 1) link_ALPHA1-3 : bond 0.00881 ( 5) link_ALPHA1-3 : angle 1.58511 ( 15) link_ALPHA1-6 : bond 0.01008 ( 4) link_ALPHA1-6 : angle 2.08454 ( 12) link_BETA1-4 : bond 0.00381 ( 11) link_BETA1-4 : angle 2.16275 ( 33) link_NAG-ASN : bond 0.00439 ( 7) link_NAG-ASN : angle 4.75150 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: C 329 MET cc_start: 0.7132 (mtt) cc_final: 0.6763 (mtp) REVERT: C 398 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7763 (mt-10) REVERT: E 24 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7836 (mm-30) REVERT: E 313 SER cc_start: 0.8419 (m) cc_final: 0.8218 (p) REVERT: E 452 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: D 167 LYS cc_start: 0.7256 (ttmm) cc_final: 0.7020 (tttm) REVERT: D 186 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: B 272 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: F 41 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7444 (mmt-90) REVERT: F 154 SER cc_start: 0.6536 (m) cc_final: 0.6171 (p) REVERT: F 242 HIS cc_start: 0.5462 (t-90) cc_final: 0.5232 (t-170) outliers start: 11 outliers final: 3 residues processed: 238 average time/residue: 1.2714 time to fit residues: 341.8261 Evaluate side-chains 230 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 191 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 219 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN D 475 GLN F 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104832 restraints weight = 58086.104| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.86 r_work: 0.3133 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20978 Z= 0.218 Angle : 0.606 15.003 28666 Z= 0.310 Chirality : 0.045 0.254 3391 Planarity : 0.005 0.070 3492 Dihedral : 8.756 95.235 3720 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 0.67 % Allowed : 10.95 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.42 (0.17), residues: 2445 helix: 2.49 (0.17), residues: 806 sheet: 0.50 (0.20), residues: 628 loop : 0.03 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 209 TYR 0.017 0.002 TYR E 225 PHE 0.022 0.002 PHE C 284 TRP 0.020 0.002 TRP D 176 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00492 (20940) covalent geometry : angle 0.58060 (28565) SS BOND : bond 0.00572 ( 10) SS BOND : angle 1.52127 ( 20) hydrogen bonds : bond 0.05501 ( 1018) hydrogen bonds : angle 4.54984 ( 3123) Misc. bond : bond 0.00092 ( 1) link_ALPHA1-3 : bond 0.00877 ( 5) link_ALPHA1-3 : angle 1.52172 ( 15) link_ALPHA1-6 : bond 0.00971 ( 4) link_ALPHA1-6 : angle 2.06848 ( 12) link_BETA1-4 : bond 0.00505 ( 11) link_BETA1-4 : angle 2.45917 ( 33) link_NAG-ASN : bond 0.00681 ( 7) link_NAG-ASN : angle 5.14924 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: C 241 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 329 MET cc_start: 0.7172 (mtt) cc_final: 0.6813 (mtp) REVERT: C 398 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7790 (mt-10) REVERT: E 6 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8393 (mtm110) REVERT: E 24 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7796 (mm-30) REVERT: E 452 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: D 86 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8535 (mtp) REVERT: D 167 LYS cc_start: 0.7322 (ttmm) cc_final: 0.7080 (tttm) REVERT: D 186 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: B 272 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: B 316 HIS cc_start: 0.7298 (m90) cc_final: 0.6675 (m90) REVERT: F 154 SER cc_start: 0.6534 (m) cc_final: 0.6175 (p) outliers start: 15 outliers final: 5 residues processed: 244 average time/residue: 1.1757 time to fit residues: 324.5183 Evaluate side-chains 237 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 228 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 233 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 227 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN E 131 GLN D 475 GLN F 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106220 restraints weight = 58071.983| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.61 r_work: 0.3174 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20978 Z= 0.117 Angle : 0.515 9.776 28666 Z= 0.264 Chirality : 0.043 0.212 3391 Planarity : 0.004 0.051 3492 Dihedral : 8.106 85.654 3720 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 0.36 % Allowed : 11.39 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2445 helix: 2.66 (0.18), residues: 812 sheet: 0.52 (0.20), residues: 633 loop : 0.13 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 20 TYR 0.013 0.001 TYR F 187 PHE 0.018 0.001 PHE C 284 TRP 0.014 0.001 TRP B 55 HIS 0.009 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00248 (20940) covalent geometry : angle 0.50037 (28565) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.74024 ( 20) hydrogen bonds : bond 0.04675 ( 1018) hydrogen bonds : angle 4.33166 ( 3123) Misc. bond : bond 0.00063 ( 1) link_ALPHA1-3 : bond 0.00770 ( 5) link_ALPHA1-3 : angle 1.61477 ( 15) link_ALPHA1-6 : bond 0.01064 ( 4) link_ALPHA1-6 : angle 1.93442 ( 12) link_BETA1-4 : bond 0.00314 ( 11) link_BETA1-4 : angle 1.92198 ( 33) link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 3.36608 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 329 MET cc_start: 0.7112 (mtt) cc_final: 0.6738 (mtp) REVERT: C 398 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7770 (mt-10) REVERT: E 6 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8420 (mtm110) REVERT: E 24 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7823 (mm-30) REVERT: E 452 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: D 167 LYS cc_start: 0.7254 (ttmm) cc_final: 0.7025 (tttm) REVERT: D 186 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: F 154 SER cc_start: 0.6527 (m) cc_final: 0.6169 (p) outliers start: 8 outliers final: 6 residues processed: 233 average time/residue: 1.6006 time to fit residues: 424.2194 Evaluate side-chains 230 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 126 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 GLN D 475 GLN F 147 GLN G 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105734 restraints weight = 58389.156| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.07 r_work: 0.3149 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20978 Z= 0.156 Angle : 0.542 8.886 28666 Z= 0.279 Chirality : 0.043 0.201 3391 Planarity : 0.004 0.053 3492 Dihedral : 8.184 85.787 3720 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 0.49 % Allowed : 11.26 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.54 (0.17), residues: 2445 helix: 2.61 (0.17), residues: 812 sheet: 0.51 (0.20), residues: 633 loop : 0.11 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 209 TYR 0.013 0.001 TYR F 187 PHE 0.022 0.002 PHE C 284 TRP 0.015 0.001 TRP D 176 HIS 0.009 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00345 (20940) covalent geometry : angle 0.52710 (28565) SS BOND : bond 0.00386 ( 10) SS BOND : angle 1.13307 ( 20) hydrogen bonds : bond 0.04995 ( 1018) hydrogen bonds : angle 4.39288 ( 3123) Misc. bond : bond 0.00074 ( 1) link_ALPHA1-3 : bond 0.00801 ( 5) link_ALPHA1-3 : angle 1.49179 ( 15) link_ALPHA1-6 : bond 0.00977 ( 4) link_ALPHA1-6 : angle 1.87883 ( 12) link_BETA1-4 : bond 0.00376 ( 11) link_BETA1-4 : angle 2.17143 ( 33) link_NAG-ASN : bond 0.00325 ( 7) link_NAG-ASN : angle 3.37431 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15925.52 seconds wall clock time: 269 minutes 9.13 seconds (16149.13 seconds total)