Starting phenix.real_space_refine on Wed Aug 27 02:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432.map" model { file = "/net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nk7_12432/08_2025/7nk7_12432_trim.cif" } resolution = 2.11 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= 0.002 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 14203 2.51 5 N 3932 2.21 5 O 4892 1.98 5 H 22525 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s 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: 45644 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7470 Classifications: {'peptide': 493} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "B" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7345 Classifications: {'peptide': 483} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 7382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7382 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 464} Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7145 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1411 Classifications: {'peptide': 92} Link IDs: {'TRANS': 91} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 11.08, per 1000 atoms: 0.24 Number of scatterers: 45644 At special positions: 0 Unit cell: (117.03, 129.48, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 71 16.00 P 16 15.00 Mg 5 11.99 O 4892 8.00 N 3932 7.00 C 14203 6.00 H 22525 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5356 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 19 sheets defined 50.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.643A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 250 - end of helix removed outlier: 3.655A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 414 through 432 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.396A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.057A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.546A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.672A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.559A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 311 removed outlier: 3.700A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 383 through 406 removed outlier: 4.968A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.551A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.786A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.880A pdb=" N LYS C 84 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.890A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.886A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.769A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.584A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.625A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.675A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.600A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.769A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.920A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.846A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 317 through 325 removed outlier: 4.391A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.553A pdb=" N LYS D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 390 removed outlier: 4.751A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 413 removed outlier: 3.644A pdb=" N SER D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 181 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.759A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 317 through 325 Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 362 through 389 removed outlier: 4.424A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 395 through 412 Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.633A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.877A pdb=" N PHE E 456 " --> pdb=" O GLN E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 4.978A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.762A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 294 Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 382 Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.628A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 445 Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 460 through 472 Processing helix chain 'G' and resid 4 through 35 removed outlier: 3.694A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 4.328A pdb=" N ASN G 93 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 3.926A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 96 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLU A 57 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 94 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N THR E 80 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLU E 39 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR E 82 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N HIS E 37 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA E 84 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.196A pdb=" N VAL A 111 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.284A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 77 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA B 66 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 79 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY B 64 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N THR F 80 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLU F 39 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR F 82 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N HIS F 37 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA F 84 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU F 23 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL F 12 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.401A pdb=" N VAL B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 69 removed outlier: 4.114A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU C 96 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU C 57 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR C 94 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 79 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLY C 64 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N THR D 80 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N GLU D 39 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR D 82 " --> pdb=" O HIS D 37 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N HIS D 37 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA D 84 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.132A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL C 267 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU C 327 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 269 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE C 329 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE C 271 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU C 331 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 100 removed outlier: 6.412A pdb=" N PHE D 99 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 308 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 158 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 155 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR D 331 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA D 157 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.016A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.175A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.308A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.308A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.123A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.060A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 98 through 100 removed outlier: 6.715A pdb=" N SER F 185 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL F 216 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE F 187 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY F 218 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY F 189 " --> pdb=" O GLY F 218 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL F 308 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU F 158 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR F 331 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA F 157 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.057A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3174 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: 13.89 Time building geometry restraints manager: 6.79 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: 22506 1.03 - 1.23: 132 1.23 - 1.42: 9195 1.42 - 1.61: 13602 1.61 - 1.81: 123 Bond restraints: 45558 Sorted by residual: bond pdb=" O3B ATP F 600 " pdb=" PB ATP F 600 " ideal model delta sigma weight residual 1.592 1.542 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.473 0.039 2.70e-02 1.37e+03 2.09e+00 bond pdb=" O3A ATP F 600 " pdb=" PA ATP F 600 " ideal model delta sigma weight residual 1.592 1.549 0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 45553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 81278 1.62 - 3.25: 1084 3.25 - 4.87: 137 4.87 - 6.50: 26 6.50 - 8.12: 12 Bond angle restraints: 82537 Sorted by residual: angle pdb=" N VAL C 97 " pdb=" CA VAL C 97 " pdb=" C VAL C 97 " ideal model delta sigma weight residual 110.21 106.15 4.06 1.13e+00 7.83e-01 1.29e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 128.10 -6.40 1.80e+00 3.09e-01 1.26e+01 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 128.06 -6.36 1.80e+00 3.09e-01 1.25e+01 angle pdb=" C ASP A 272 " pdb=" N ASP A 273 " pdb=" CA ASP A 273 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 1.00e+01 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.28 -5.58 1.80e+00 3.09e-01 9.59e+00 ... (remaining 82532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.09: 20273 30.09 - 60.19: 958 60.19 - 90.28: 97 90.28 - 120.38: 0 120.38 - 150.47: 2 Dihedral angle restraints: 21330 sinusoidal: 11952 harmonic: 9378 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 90.47 -150.47 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 74.22 -134.22 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" CA PHE F 217 " pdb=" C PHE F 217 " pdb=" N GLY F 218 " pdb=" CA GLY F 218 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 21327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2996 0.058 - 0.116: 502 0.116 - 0.175: 75 0.175 - 0.233: 2 0.233 - 0.291: 10 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3582 not shown) Planarity restraints: 6908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 467 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PHE B 467 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE B 467 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 468 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 317 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.86e+00 pdb=" N PRO D 318 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 318 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 318 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 289 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C GLU D 289 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU D 289 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU D 290 " -0.008 2.00e-02 2.50e+03 ... (remaining 6905 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1464 2.12 - 2.74: 85476 2.74 - 3.36: 141665 3.36 - 3.98: 191436 3.98 - 4.60: 294353 Nonbonded interactions: 714394 Sorted by model distance: nonbonded pdb=" OE1 GLU D 364 " pdb="HH12 ARG D 367 " model vdw 1.501 2.450 nonbonded pdb=" OE1 GLU E 239 " pdb="HH21 ARG E 293 " model vdw 1.528 2.450 nonbonded pdb=" HZ3 LYS E 113 " pdb=" O HOH E 701 " model vdw 1.546 2.450 nonbonded pdb=" H GLY A 61 " pdb=" O HOH A 710 " model vdw 1.558 2.450 nonbonded pdb="HH22 ARG C 466 " pdb=" O GLN C 512 " model vdw 1.574 2.450 ... (remaining 714389 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 29 through 406 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 418 through 514 or resid 600 through 601)) selection = (chain 'B' and (resid 29 through 514 or resid 600 through 601)) selection = (chain 'C' and (resid 29 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 260 through 406 or (resid 417 and (name N or name CA or name C o \ r name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) \ or resid 418 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and (resid 8 through 364 or (resid 365 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 366 through 452 or resid 455 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 13.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 51.000 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23033 Z= 0.262 Angle : 0.629 8.125 31229 Z= 0.331 Chirality : 0.047 0.291 3585 Planarity : 0.005 0.042 4091 Dihedral : 16.918 150.471 8629 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.13 % Rotamer: Outliers : 0.88 % Allowed : 11.20 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.16), residues: 2937 helix: 1.16 (0.15), residues: 1210 sheet: 0.08 (0.24), residues: 456 loop : 0.73 (0.19), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 133 TYR 0.010 0.002 TYR B 262 PHE 0.018 0.002 PHE F 257 TRP 0.010 0.002 TRP C 193 HIS 0.007 0.002 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00581 (23033) covalent geometry : angle 0.62857 (31229) hydrogen bonds : bond 0.13052 ( 1151) hydrogen bonds : angle 6.60602 ( 3174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.255 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 216 average time/residue: 1.8851 time to fit residues: 452.7638 Evaluate side-chains 203 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.073945 restraints weight = 89336.534| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.25 r_work: 0.2793 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.0430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23033 Z= 0.244 Angle : 0.608 8.633 31229 Z= 0.323 Chirality : 0.044 0.169 3585 Planarity : 0.005 0.044 4091 Dihedral : 9.406 145.067 3346 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % Rotamer: Outliers : 1.25 % Allowed : 10.61 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.11 (0.15), residues: 2937 helix: 1.37 (0.15), residues: 1209 sheet: -0.05 (0.23), residues: 448 loop : 0.60 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 75 TYR 0.012 0.002 TYR A 436 PHE 0.018 0.002 PHE F 257 TRP 0.010 0.001 TRP C 193 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00529 (23033) covalent geometry : angle 0.60841 (31229) hydrogen bonds : bond 0.06171 ( 1151) hydrogen bonds : angle 5.70884 ( 3174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.371 Fit side-chains REVERT: A 436 TYR cc_start: 0.8834 (m-80) cc_final: 0.8613 (m-80) REVERT: B 396 ASP cc_start: 0.7004 (m-30) cc_final: 0.6765 (m-30) REVERT: G 7 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7290 (tt0) outliers start: 30 outliers final: 12 residues processed: 221 average time/residue: 1.8441 time to fit residues: 453.3290 Evaluate side-chains 200 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 13 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 272 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 176 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 505 ASN D 247 GLN G 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075879 restraints weight = 92590.370| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.28 r_work: 0.2829 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23033 Z= 0.136 Angle : 0.537 8.014 31229 Z= 0.280 Chirality : 0.042 0.168 3585 Planarity : 0.004 0.040 4091 Dihedral : 8.957 139.594 3338 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.50 % Favored : 98.43 % Rotamer: Outliers : 0.71 % Allowed : 11.32 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.23 (0.16), residues: 2937 helix: 1.63 (0.15), residues: 1210 sheet: -0.22 (0.23), residues: 445 loop : 0.58 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 298 TYR 0.009 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00286 (23033) covalent geometry : angle 0.53699 (31229) hydrogen bonds : bond 0.04978 ( 1151) hydrogen bonds : angle 5.42359 ( 3174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.126 Fit side-chains REVERT: A 436 TYR cc_start: 0.8807 (m-80) cc_final: 0.8562 (m-80) REVERT: B 396 ASP cc_start: 0.6962 (m-30) cc_final: 0.6654 (m-30) REVERT: C 443 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8208 (mt-10) outliers start: 17 outliers final: 8 residues processed: 214 average time/residue: 2.0027 time to fit residues: 475.7920 Evaluate side-chains 197 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 187 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075197 restraints weight = 100136.911| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.34 r_work: 0.2814 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23033 Z= 0.162 Angle : 0.542 8.266 31229 Z= 0.284 Chirality : 0.042 0.158 3585 Planarity : 0.004 0.040 4091 Dihedral : 8.817 127.659 3332 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.30 % Rotamer: Outliers : 0.84 % Allowed : 11.12 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.22 (0.16), residues: 2937 helix: 1.68 (0.15), residues: 1212 sheet: -0.36 (0.23), residues: 435 loop : 0.55 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 133 TYR 0.009 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00347 (23033) covalent geometry : angle 0.54207 (31229) hydrogen bonds : bond 0.05068 ( 1151) hydrogen bonds : angle 5.35191 ( 3174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.221 Fit side-chains REVERT: A 214 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 436 TYR cc_start: 0.8823 (m-80) cc_final: 0.8569 (m-80) REVERT: B 396 ASP cc_start: 0.6984 (m-30) cc_final: 0.6657 (m-30) outliers start: 20 outliers final: 9 residues processed: 216 average time/residue: 1.8770 time to fit residues: 453.5619 Evaluate side-chains 200 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 93 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.074243 restraints weight = 89311.933| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.25 r_work: 0.2799 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23033 Z= 0.240 Angle : 0.591 8.807 31229 Z= 0.312 Chirality : 0.044 0.169 3585 Planarity : 0.004 0.051 4091 Dihedral : 8.955 118.133 3330 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.30 % Rotamer: Outliers : 0.92 % Allowed : 11.20 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.10 (0.15), residues: 2937 helix: 1.53 (0.15), residues: 1213 sheet: -0.32 (0.23), residues: 437 loop : 0.51 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 133 TYR 0.010 0.002 TYR A 436 PHE 0.018 0.002 PHE F 257 TRP 0.009 0.001 TRP C 193 HIS 0.008 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00526 (23033) covalent geometry : angle 0.59068 (31229) hydrogen bonds : bond 0.05747 ( 1151) hydrogen bonds : angle 5.45798 ( 3174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.092 Fit side-chains REVERT: A 436 TYR cc_start: 0.8861 (m-80) cc_final: 0.8569 (m-80) REVERT: B 396 ASP cc_start: 0.6975 (m-30) cc_final: 0.6636 (m-30) REVERT: B 403 LEU cc_start: 0.7602 (tt) cc_final: 0.6968 (tp) REVERT: C 387 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8039 (mtmm) REVERT: G 7 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7288 (tt0) outliers start: 22 outliers final: 16 residues processed: 217 average time/residue: 1.4308 time to fit residues: 348.5832 Evaluate side-chains 206 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 3 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.074982 restraints weight = 93888.794| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.29 r_work: 0.2811 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23033 Z= 0.174 Angle : 0.555 8.413 31229 Z= 0.292 Chirality : 0.042 0.168 3585 Planarity : 0.004 0.046 4091 Dihedral : 8.787 109.331 3330 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.30 % Rotamer: Outliers : 0.96 % Allowed : 11.32 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.15 (0.15), residues: 2937 helix: 1.62 (0.15), residues: 1213 sheet: -0.39 (0.23), residues: 437 loop : 0.52 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 133 TYR 0.009 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.008 0.001 TRP C 193 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00373 (23033) covalent geometry : angle 0.55536 (31229) hydrogen bonds : bond 0.05211 ( 1151) hydrogen bonds : angle 5.36679 ( 3174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.762 Fit side-chains REVERT: A 214 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 436 TYR cc_start: 0.8858 (m-80) cc_final: 0.8549 (m-80) REVERT: B 350 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8873 (m-30) REVERT: B 396 ASP cc_start: 0.6976 (m-30) cc_final: 0.6624 (m-30) REVERT: C 387 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8003 (mtmm) REVERT: G 7 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7293 (tt0) outliers start: 23 outliers final: 14 residues processed: 213 average time/residue: 1.1710 time to fit residues: 280.6550 Evaluate side-chains 203 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 187 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 291 optimal weight: 0.3980 chunk 164 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075855 restraints weight = 89083.251| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.26 r_work: 0.2830 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23033 Z= 0.149 Angle : 0.537 8.230 31229 Z= 0.280 Chirality : 0.042 0.163 3585 Planarity : 0.004 0.046 4091 Dihedral : 8.613 108.495 3330 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 0.84 % Allowed : 11.28 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.23 (0.16), residues: 2937 helix: 1.73 (0.15), residues: 1213 sheet: -0.45 (0.23), residues: 435 loop : 0.55 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 133 TYR 0.008 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00320 (23033) covalent geometry : angle 0.53711 (31229) hydrogen bonds : bond 0.04884 ( 1151) hydrogen bonds : angle 5.27294 ( 3174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.777 Fit side-chains REVERT: A 214 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 436 TYR cc_start: 0.8845 (m-80) cc_final: 0.8558 (m-80) REVERT: B 350 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8861 (m-30) REVERT: B 396 ASP cc_start: 0.7015 (m-30) cc_final: 0.6663 (m-30) REVERT: C 387 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7983 (mtmm) outliers start: 20 outliers final: 11 residues processed: 211 average time/residue: 1.1160 time to fit residues: 265.4929 Evaluate side-chains 200 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 267 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 420 GLN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.074916 restraints weight = 90558.411| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.27 r_work: 0.2811 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23033 Z= 0.196 Angle : 0.564 8.630 31229 Z= 0.296 Chirality : 0.043 0.165 3585 Planarity : 0.004 0.051 4091 Dihedral : 8.699 108.621 3325 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.53 % Favored : 98.43 % Rotamer: Outliers : 0.79 % Allowed : 11.58 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.17 (0.15), residues: 2937 helix: 1.64 (0.15), residues: 1213 sheet: -0.43 (0.23), residues: 438 loop : 0.54 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 133 TYR 0.009 0.001 TYR B 262 PHE 0.017 0.002 PHE F 257 TRP 0.008 0.001 TRP C 193 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00425 (23033) covalent geometry : angle 0.56391 (31229) hydrogen bonds : bond 0.05323 ( 1151) hydrogen bonds : angle 5.34298 ( 3174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.779 Fit side-chains REVERT: A 214 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8952 (p) REVERT: A 436 TYR cc_start: 0.8861 (m-80) cc_final: 0.8566 (m-80) REVERT: B 350 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8880 (m-30) REVERT: B 396 ASP cc_start: 0.7029 (m-30) cc_final: 0.6681 (m-30) REVERT: C 387 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7990 (mtmm) outliers start: 19 outliers final: 13 residues processed: 210 average time/residue: 1.1412 time to fit residues: 269.8253 Evaluate side-chains 206 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 168 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 505 ASN D 247 GLN E 175 ASN E 453 GLN G 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075253 restraints weight = 95079.584| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.30 r_work: 0.2817 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23033 Z= 0.170 Angle : 0.551 8.389 31229 Z= 0.288 Chirality : 0.042 0.164 3585 Planarity : 0.004 0.049 4091 Dihedral : 8.634 108.519 3325 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.26 % Rotamer: Outliers : 0.67 % Allowed : 11.70 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.19 (0.16), residues: 2937 helix: 1.69 (0.15), residues: 1213 sheet: -0.46 (0.23), residues: 437 loop : 0.55 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 133 TYR 0.008 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00365 (23033) covalent geometry : angle 0.55127 (31229) hydrogen bonds : bond 0.05082 ( 1151) hydrogen bonds : angle 5.30397 ( 3174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.767 Fit side-chains REVERT: A 214 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 436 TYR cc_start: 0.8848 (m-80) cc_final: 0.8544 (m-80) REVERT: B 350 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8873 (m-30) REVERT: B 396 ASP cc_start: 0.7032 (m-30) cc_final: 0.6670 (m-30) REVERT: C 387 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7965 (mtmm) outliers start: 16 outliers final: 12 residues processed: 203 average time/residue: 1.1067 time to fit residues: 253.0432 Evaluate side-chains 202 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 188 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075572 restraints weight = 88549.853| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.25 r_work: 0.2824 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23033 Z= 0.167 Angle : 0.549 8.368 31229 Z= 0.287 Chirality : 0.042 0.163 3585 Planarity : 0.004 0.048 4091 Dihedral : 8.594 108.307 3324 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.36 % Rotamer: Outliers : 0.67 % Allowed : 11.70 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.20 (0.16), residues: 2937 helix: 1.70 (0.15), residues: 1213 sheet: -0.48 (0.23), residues: 437 loop : 0.55 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 133 TYR 0.008 0.001 TYR B 262 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00361 (23033) covalent geometry : angle 0.54885 (31229) hydrogen bonds : bond 0.05050 ( 1151) hydrogen bonds : angle 5.28888 ( 3174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.735 Fit side-chains REVERT: A 214 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 436 TYR cc_start: 0.8843 (m-80) cc_final: 0.8540 (m-80) REVERT: B 350 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: B 396 ASP cc_start: 0.7038 (m-30) cc_final: 0.6671 (m-30) REVERT: C 387 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: G 7 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7267 (tt0) outliers start: 16 outliers final: 11 residues processed: 204 average time/residue: 1.0807 time to fit residues: 249.0822 Evaluate side-chains 204 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 207 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 253 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 505 ASN D 247 GLN E 453 GLN G 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.075948 restraints weight = 92871.403| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.29 r_work: 0.2830 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23033 Z= 0.148 Angle : 0.538 8.234 31229 Z= 0.281 Chirality : 0.042 0.161 3585 Planarity : 0.004 0.044 4091 Dihedral : 8.498 107.813 3322 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.36 % Rotamer: Outliers : 0.50 % Allowed : 11.95 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.25 (0.16), residues: 2937 helix: 1.77 (0.15), residues: 1213 sheet: -0.50 (0.23), residues: 436 loop : 0.56 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 133 TYR 0.007 0.001 TYR A 436 PHE 0.017 0.001 PHE F 257 TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00316 (23033) covalent geometry : angle 0.53848 (31229) hydrogen bonds : bond 0.04822 ( 1151) hydrogen bonds : angle 5.24043 ( 3174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13587.19 seconds wall clock time: 229 minutes 52.95 seconds (13792.95 seconds total)