Starting phenix.real_space_refine on Wed Feb 4 19:36:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.map" model { file = "/net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yy4_39666/02_2026/8yy4_39666.cif" } resolution = 4.02 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= 0.001 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 9 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 7699 2.51 5 N 2134 2.21 5 O 2384 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12315 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3352 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3356 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2836 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 11, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2650 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12315 At special positions: 0 Unit cell: (100.016, 128.592, 117.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 82 16.00 P 9 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2384 8.00 N 2134 7.00 C 7699 6.00 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 Atom "HETATM12276 O3A ADP C 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 362.7 milliseconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 49.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.030A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.429A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.723A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.529A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.824A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.639A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.704A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 4.224A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.814A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.534A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.233A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.311A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.703A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 108 through 127 removed outlier: 5.360A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.861A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.528A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.521A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.705A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.603A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.529A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.311A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 4.195A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 346 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 385 through 391 Processing helix chain 'C' and resid 407 through 413 removed outlier: 3.616A pdb=" N ILE C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.736A pdb=" N LEU C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.612A pdb=" N ARG C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.907A pdb=" N SER C 553 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 615 Processing helix chain 'C' and resid 625 through 631 Processing helix chain 'C' and resid 631 through 636 Processing helix chain 'C' and resid 650 through 652 No H-bonds generated for 'chain 'C' and resid 650 through 652' Processing helix chain 'C' and resid 653 through 669 Processing helix chain 'D' and resid 326 through 347 Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.644A pdb=" N SER D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.585A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 469 removed outlier: 3.686A pdb=" N ARG D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 540 removed outlier: 3.778A pdb=" N ALA D 540 " --> pdb=" O LYS D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.841A pdb=" N ASN D 624 " --> pdb=" O PRO D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 625 through 631 Processing helix chain 'D' and resid 632 through 636 removed outlier: 4.049A pdb=" N GLY D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 669 removed outlier: 3.818A pdb=" N LYS D 659 " --> pdb=" O GLN D 655 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 667 " --> pdb=" O PHE D 663 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 9.011A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.808A pdb=" N CYS A 316 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.465A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 55 removed outlier: 6.894A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 removed outlier: 5.946A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 400 through 402 removed outlier: 8.619A pdb=" N GLN C 400 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C 351 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N PHE C 402 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS C 353 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 432 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 488 through 490 removed outlier: 3.706A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 371 through 374 removed outlier: 6.486A pdb=" N THR C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 502 through 504 Processing sheet with id=AB2, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.942A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 432 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.942A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 432 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 477 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 520 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 369 through 372 Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 504 655 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4076 1.34 - 1.46: 2396 1.46 - 1.58: 5940 1.58 - 1.70: 16 1.70 - 1.82: 135 Bond restraints: 12563 Sorted by residual: bond pdb=" F4 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.686 1.733 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" CA PRO A 359 " pdb=" C PRO A 359 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 4.07e+00 bond pdb=" CB CYS B 12 " pdb=" SG CYS B 12 " ideal model delta sigma weight residual 1.808 1.742 0.066 3.30e-02 9.18e+02 4.05e+00 bond pdb=" F3 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.685 1.720 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" CA PRO D 357 " pdb=" C PRO D 357 " ideal model delta sigma weight residual 1.517 1.505 0.012 6.70e-03 2.23e+04 3.00e+00 ... (remaining 12558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 17012 6.68 - 13.37: 5 13.37 - 20.05: 0 20.05 - 26.74: 3 26.74 - 33.42: 3 Bond angle restraints: 17023 Sorted by residual: angle pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " pdb=" F3 ALF C 903 " ideal model delta sigma weight residual 109.69 76.27 33.42 3.00e+00 1.11e-01 1.24e+02 angle pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " pdb=" F4 ALF C 903 " ideal model delta sigma weight residual 109.02 78.56 30.46 3.00e+00 1.11e-01 1.03e+02 angle pdb=" F3 ALF C 903 " pdb="AL ALF C 903 " pdb=" F4 ALF C 903 " ideal model delta sigma weight residual 109.63 139.75 -30.12 3.00e+00 1.11e-01 1.01e+02 angle pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " pdb=" F2 ALF C 903 " ideal model delta sigma weight residual 108.68 135.09 -26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" F2 ALF C 903 " pdb="AL ALF C 903 " pdb=" F4 ALF C 903 " ideal model delta sigma weight residual 110.21 86.99 23.22 3.00e+00 1.11e-01 5.99e+01 ... (remaining 17018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 7466 35.79 - 71.57: 97 71.57 - 107.36: 5 107.36 - 143.14: 1 143.14 - 178.93: 2 Dihedral angle restraints: 7571 sinusoidal: 3080 harmonic: 4491 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -111.80 -178.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 97.15 176.97 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -34.59 139.18 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 7568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1350 0.043 - 0.086: 399 0.086 - 0.129: 126 0.129 - 0.172: 9 0.172 - 0.215: 3 Chirality restraints: 1887 Sorted by residual: chirality pdb=" C3' GDP B 501 " pdb=" C4' GDP B 501 " pdb=" O3' GDP B 501 " pdb=" C2' GDP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C2' ADP C 901 " pdb=" C1' ADP C 901 " pdb=" C3' ADP C 901 " pdb=" O2' ADP C 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1884 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP B 501 " 0.030 2.00e-02 2.50e+03 1.66e-02 8.23e+00 pdb=" N9 GDP B 501 " -0.030 2.00e-02 2.50e+03 pdb=" C8 GDP B 501 " -0.016 2.00e-02 2.50e+03 pdb=" N7 GDP B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C5 GDP B 501 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GDP B 501 " 0.008 2.00e-02 2.50e+03 pdb=" O6 GDP B 501 " 0.015 2.00e-02 2.50e+03 pdb=" N1 GDP B 501 " -0.000 2.00e-02 2.50e+03 pdb=" C2 GDP B 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 GDP B 501 " -0.013 2.00e-02 2.50e+03 pdb=" N3 GDP B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 GDP B 501 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 403 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO C 404 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 145 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C THR A 145 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 145 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 146 " -0.011 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 192 2.56 - 3.15: 10942 3.15 - 3.73: 21090 3.73 - 4.32: 28437 4.32 - 4.90: 44740 Nonbonded interactions: 105401 Sorted by model distance: nonbonded pdb=" O3B ADP C 901 " pdb=" F3 ALF C 903 " model vdw 1.977 2.990 nonbonded pdb=" O GLN B 334 " pdb=" OG SER B 338 " model vdw 2.020 3.040 nonbonded pdb="MG MG C 902 " pdb=" F1 ALF C 903 " model vdw 2.039 2.120 nonbonded pdb=" O VAL A 288 " pdb=" OG1 THR A 292 " model vdw 2.063 3.040 nonbonded pdb=" OG SER B 145 " pdb=" OG SER B 188 " model vdw 2.084 3.040 ... (remaining 105396 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 'C' and (resid 325 through 587 or resid 599 through 617 or (resid 618 and \ (name N or name CA or name C or name O or name CB )) or resid 619 through 669 o \ r resid 902)) selection = (chain 'D' and (resid 325 through 542 or resid 548 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 14.390 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3611 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 : 0.004 0.066 12563 Z= 0.214 Angle : 0.851 33.422 17023 Z= 0.387 Chirality : 0.044 0.215 1887 Planarity : 0.005 0.052 2202 Dihedral : 13.206 178.927 4671 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.11 % Allowed : 7.62 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1531 helix: 0.69 (0.20), residues: 653 sheet: 0.04 (0.38), residues: 226 loop : -1.28 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 350 TYR 0.014 0.002 TYR A 24 PHE 0.022 0.002 PHE B 20 TRP 0.015 0.002 TRP A 21 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00442 (12563) covalent geometry : angle 0.85091 (17023) hydrogen bonds : bond 0.17014 ( 599) hydrogen bonds : angle 7.21276 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.5924 (t80) cc_final: 0.5714 (t80) REVERT: A 138 PHE cc_start: 0.8658 (m-10) cc_final: 0.8249 (m-10) REVERT: A 286 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 313 MET cc_start: 0.8789 (mpp) cc_final: 0.7980 (mpp) REVERT: A 372 GLN cc_start: 0.9115 (mm110) cc_final: 0.8899 (pm20) REVERT: A 373 ARG cc_start: 0.9079 (ptp-170) cc_final: 0.8500 (ptp-170) REVERT: B 22 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 37 HIS cc_start: 0.8585 (m-70) cc_final: 0.8335 (m-70) REVERT: B 50 TYR cc_start: 0.8989 (m-80) cc_final: 0.8710 (m-10) REVERT: B 208 TYR cc_start: -0.0705 (OUTLIER) cc_final: -0.1990 (m-80) REVERT: B 257 MET cc_start: 0.8570 (mmm) cc_final: 0.8333 (mmm) REVERT: B 267 MET cc_start: 0.8607 (ttm) cc_final: 0.8016 (ttt) REVERT: B 300 MET cc_start: 0.8122 (mmt) cc_final: 0.7695 (mmt) REVERT: B 307 HIS cc_start: 0.9001 (m90) cc_final: 0.8586 (m-70) REVERT: B 376 GLU cc_start: 0.8904 (mp0) cc_final: 0.8592 (mp0) REVERT: B 394 PHE cc_start: 0.0367 (OUTLIER) cc_final: -0.0026 (m-10) REVERT: B 403 MET cc_start: 0.6810 (mmm) cc_final: 0.6552 (mmm) REVERT: C 500 MET cc_start: 0.6700 (mmt) cc_final: 0.5937 (mmt) REVERT: D 632 MET cc_start: 0.3471 (mmt) cc_final: 0.3150 (mmt) outliers start: 42 outliers final: 23 residues processed: 251 average time/residue: 0.1040 time to fit residues: 37.9146 Evaluate side-chains 190 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 40.0000 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 ASN C 554 HIS C 624 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 ASN D 565 HIS D 600 ASN D 646 ASN D 651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.213473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.089468 restraints weight = 52598.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.090879 restraints weight = 35891.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.089786 restraints weight = 27716.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.089786 restraints weight = 24901.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.089786 restraints weight = 24901.974| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12563 Z= 0.178 Angle : 0.853 31.756 17023 Z= 0.385 Chirality : 0.046 0.152 1887 Planarity : 0.005 0.061 2202 Dihedral : 9.219 177.453 1720 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1531 helix: 0.50 (0.20), residues: 654 sheet: 0.11 (0.38), residues: 224 loop : -1.28 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 121 TYR 0.026 0.002 TYR A 83 PHE 0.040 0.002 PHE B 212 TRP 0.026 0.001 TRP A 21 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00376 (12563) covalent geometry : angle 0.85254 (17023) hydrogen bonds : bond 0.04384 ( 599) hydrogen bonds : angle 5.49380 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9299 (mt) cc_final: 0.9085 (mt) REVERT: A 103 TYR cc_start: 0.6569 (t80) cc_final: 0.6158 (t80) REVERT: A 138 PHE cc_start: 0.8746 (m-10) cc_final: 0.8296 (m-10) REVERT: A 286 LEU cc_start: 0.8750 (mm) cc_final: 0.8171 (mm) REVERT: A 313 MET cc_start: 0.9191 (mpp) cc_final: 0.8178 (mpp) REVERT: A 370 LYS cc_start: 0.9246 (tptp) cc_final: 0.9038 (tptp) REVERT: A 373 ARG cc_start: 0.8999 (ptp-170) cc_final: 0.8594 (ptp-170) REVERT: B 19 LYS cc_start: 0.8758 (tttt) cc_final: 0.8532 (tttt) REVERT: B 37 HIS cc_start: 0.8803 (m-70) cc_final: 0.8538 (m-70) REVERT: B 45 ASP cc_start: 0.9030 (t70) cc_final: 0.8781 (m-30) REVERT: B 224 ASP cc_start: 0.8648 (m-30) cc_final: 0.8334 (m-30) REVERT: B 267 MET cc_start: 0.8806 (ttm) cc_final: 0.8130 (ttt) REVERT: B 307 HIS cc_start: 0.9090 (m90) cc_final: 0.8635 (m-70) REVERT: B 376 GLU cc_start: 0.9001 (mp0) cc_final: 0.8720 (mp0) REVERT: C 402 PHE cc_start: 0.4323 (m-80) cc_final: 0.3242 (m-80) REVERT: C 489 LEU cc_start: 0.5689 (mp) cc_final: 0.5415 (mp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1085 time to fit residues: 32.6676 Evaluate side-chains 163 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.199970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.123851 restraints weight = 34218.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.110009 restraints weight = 30083.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.110732 restraints weight = 20469.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.109793 restraints weight = 15989.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.109942 restraints weight = 14494.914| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12563 Z= 0.154 Angle : 0.832 30.038 17023 Z= 0.374 Chirality : 0.046 0.310 1887 Planarity : 0.005 0.048 2202 Dihedral : 9.171 178.232 1720 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1531 helix: 0.46 (0.20), residues: 660 sheet: 0.20 (0.38), residues: 221 loop : -1.27 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 121 TYR 0.018 0.001 TYR A 83 PHE 0.027 0.002 PHE B 20 TRP 0.029 0.001 TRP A 21 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00321 (12563) covalent geometry : angle 0.83163 (17023) hydrogen bonds : bond 0.04089 ( 599) hydrogen bonds : angle 5.25474 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.6760 (t80) cc_final: 0.6364 (t80) REVERT: A 138 PHE cc_start: 0.8694 (m-10) cc_final: 0.8298 (m-10) REVERT: A 167 LEU cc_start: 0.9207 (tp) cc_final: 0.8839 (tp) REVERT: A 169 PHE cc_start: 0.8795 (t80) cc_final: 0.8586 (t80) REVERT: A 286 LEU cc_start: 0.8717 (mm) cc_final: 0.8495 (mm) REVERT: A 313 MET cc_start: 0.9194 (mpp) cc_final: 0.7976 (mpp) REVERT: B 14 ASN cc_start: 0.9006 (m-40) cc_final: 0.8652 (t0) REVERT: B 37 HIS cc_start: 0.8887 (m-70) cc_final: 0.8606 (m-70) REVERT: B 41 ASP cc_start: 0.9420 (p0) cc_final: 0.9219 (p0) REVERT: B 45 ASP cc_start: 0.9156 (t70) cc_final: 0.8794 (m-30) REVERT: B 224 ASP cc_start: 0.8666 (m-30) cc_final: 0.8349 (m-30) REVERT: B 267 MET cc_start: 0.8718 (ttm) cc_final: 0.8120 (ttt) REVERT: B 307 HIS cc_start: 0.9071 (m90) cc_final: 0.8610 (m-70) REVERT: B 376 GLU cc_start: 0.8781 (mp0) cc_final: 0.8467 (mp0) REVERT: B 403 MET cc_start: 0.7977 (tpt) cc_final: 0.7456 (mmm) REVERT: C 402 PHE cc_start: 0.3915 (m-80) cc_final: 0.3611 (m-80) REVERT: C 412 PHE cc_start: 0.7691 (t80) cc_final: 0.7326 (t80) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0936 time to fit residues: 27.8654 Evaluate side-chains 165 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 102 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 129 optimal weight: 50.0000 chunk 141 optimal weight: 40.0000 chunk 45 optimal weight: 0.0870 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.202478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.109378 restraints weight = 33647.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.109060 restraints weight = 22016.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.111065 restraints weight = 17754.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.111033 restraints weight = 15810.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.110887 restraints weight = 14851.864| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12563 Z= 0.124 Angle : 0.818 30.087 17023 Z= 0.364 Chirality : 0.044 0.201 1887 Planarity : 0.004 0.046 2202 Dihedral : 9.090 179.589 1720 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.15 % Allowed : 2.59 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1531 helix: 0.57 (0.20), residues: 660 sheet: 0.45 (0.39), residues: 211 loop : -1.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.029 0.001 TYR A 24 PHE 0.027 0.002 PHE B 20 TRP 0.026 0.001 TRP A 21 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00258 (12563) covalent geometry : angle 0.81786 (17023) hydrogen bonds : bond 0.03790 ( 599) hydrogen bonds : angle 5.05412 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.6708 (t80) cc_final: 0.6243 (t80) REVERT: A 138 PHE cc_start: 0.8600 (m-10) cc_final: 0.8258 (m-10) REVERT: A 167 LEU cc_start: 0.9120 (tp) cc_final: 0.8548 (tp) REVERT: A 169 PHE cc_start: 0.8725 (t80) cc_final: 0.8322 (t80) REVERT: A 203 MET cc_start: 0.7198 (mmp) cc_final: 0.6756 (mmp) REVERT: A 286 LEU cc_start: 0.8726 (mm) cc_final: 0.8408 (mm) REVERT: A 313 MET cc_start: 0.9193 (mpp) cc_final: 0.8113 (mpp) REVERT: A 395 PHE cc_start: 0.8632 (t80) cc_final: 0.7969 (t80) REVERT: B 14 ASN cc_start: 0.8963 (m-40) cc_final: 0.8646 (t0) REVERT: B 37 HIS cc_start: 0.8868 (m-70) cc_final: 0.8622 (m-70) REVERT: B 45 ASP cc_start: 0.9116 (t70) cc_final: 0.8779 (m-30) REVERT: B 147 MET cc_start: 0.9413 (ppp) cc_final: 0.9106 (ppp) REVERT: B 224 ASP cc_start: 0.8685 (m-30) cc_final: 0.8407 (m-30) REVERT: B 267 MET cc_start: 0.8717 (ttm) cc_final: 0.8106 (ttt) REVERT: B 307 HIS cc_start: 0.9059 (m90) cc_final: 0.8592 (m-70) REVERT: B 376 GLU cc_start: 0.8742 (mp0) cc_final: 0.8403 (mp0) REVERT: C 402 PHE cc_start: 0.3641 (m-80) cc_final: 0.3183 (m-80) REVERT: C 412 PHE cc_start: 0.7711 (t80) cc_final: 0.7378 (t80) outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.0956 time to fit residues: 29.8948 Evaluate side-chains 171 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 146 optimal weight: 40.0000 chunk 79 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.196874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.105194 restraints weight = 34017.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.105171 restraints weight = 22442.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.104730 restraints weight = 18074.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.105796 restraints weight = 16674.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.105847 restraints weight = 15634.791| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12563 Z= 0.176 Angle : 0.838 30.019 17023 Z= 0.377 Chirality : 0.045 0.265 1887 Planarity : 0.005 0.045 2202 Dihedral : 9.086 175.843 1720 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1531 helix: 0.60 (0.20), residues: 664 sheet: 0.39 (0.39), residues: 220 loop : -1.25 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 373 TYR 0.025 0.002 TYR A 83 PHE 0.032 0.002 PHE A 418 TRP 0.044 0.002 TRP A 21 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00372 (12563) covalent geometry : angle 0.83775 (17023) hydrogen bonds : bond 0.03799 ( 599) hydrogen bonds : angle 5.03019 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7122 (t80) cc_final: 0.6689 (t80) REVERT: A 116 ASP cc_start: 0.8863 (p0) cc_final: 0.8135 (p0) REVERT: A 120 ASP cc_start: 0.8906 (m-30) cc_final: 0.8617 (m-30) REVERT: A 138 PHE cc_start: 0.8801 (m-10) cc_final: 0.8271 (m-10) REVERT: A 199 ASP cc_start: 0.9078 (m-30) cc_final: 0.8773 (m-30) REVERT: A 313 MET cc_start: 0.9173 (mpp) cc_final: 0.8134 (mpp) REVERT: A 395 PHE cc_start: 0.8690 (t80) cc_final: 0.8015 (t80) REVERT: B 37 HIS cc_start: 0.8885 (m-70) cc_final: 0.8630 (m-70) REVERT: B 45 ASP cc_start: 0.9139 (t70) cc_final: 0.8788 (m-30) REVERT: B 147 MET cc_start: 0.9390 (ppp) cc_final: 0.9129 (ppp) REVERT: B 224 ASP cc_start: 0.8821 (m-30) cc_final: 0.8554 (m-30) REVERT: B 267 MET cc_start: 0.8852 (ttm) cc_final: 0.8227 (ttt) REVERT: B 306 ARG cc_start: 0.8052 (mmp80) cc_final: 0.7574 (mmp80) REVERT: B 307 HIS cc_start: 0.9104 (m90) cc_final: 0.8654 (m-70) REVERT: B 376 GLU cc_start: 0.8783 (mp0) cc_final: 0.8451 (mp0) REVERT: B 403 MET cc_start: 0.8185 (tpt) cc_final: 0.7914 (mmm) REVERT: C 402 PHE cc_start: 0.4020 (m-80) cc_final: 0.3528 (m-80) REVERT: C 412 PHE cc_start: 0.7730 (t80) cc_final: 0.7394 (t80) REVERT: C 485 LYS cc_start: 0.4764 (tptt) cc_final: 0.4478 (tptt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1029 time to fit residues: 30.3426 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.189545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.098045 restraints weight = 34023.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.095470 restraints weight = 23798.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.095598 restraints weight = 20083.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.096040 restraints weight = 18664.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.096559 restraints weight = 17896.164| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12563 Z= 0.281 Angle : 0.925 30.016 17023 Z= 0.432 Chirality : 0.048 0.195 1887 Planarity : 0.006 0.047 2202 Dihedral : 9.385 168.709 1720 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1531 helix: 0.33 (0.20), residues: 670 sheet: 0.31 (0.39), residues: 217 loop : -1.22 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 390 TYR 0.024 0.002 TYR C 622 PHE 0.030 0.002 PHE A 255 TRP 0.057 0.003 TRP A 21 HIS 0.009 0.002 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00583 (12563) covalent geometry : angle 0.92498 (17023) hydrogen bonds : bond 0.04139 ( 599) hydrogen bonds : angle 5.20348 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7313 (t80) cc_final: 0.7016 (t80) REVERT: A 116 ASP cc_start: 0.9136 (p0) cc_final: 0.8918 (p0) REVERT: A 199 ASP cc_start: 0.9107 (m-30) cc_final: 0.8793 (m-30) REVERT: A 286 LEU cc_start: 0.9055 (mm) cc_final: 0.8853 (mm) REVERT: A 313 MET cc_start: 0.9044 (mpp) cc_final: 0.8078 (mpp) REVERT: A 316 CYS cc_start: 0.8876 (t) cc_final: 0.8634 (t) REVERT: A 358 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7866 (tp-100) REVERT: B 14 ASN cc_start: 0.9119 (m-40) cc_final: 0.8897 (m-40) REVERT: B 37 HIS cc_start: 0.8948 (m-70) cc_final: 0.8672 (m-70) REVERT: B 73 MET cc_start: 0.9410 (mpp) cc_final: 0.8417 (mpp) REVERT: B 224 ASP cc_start: 0.8784 (m-30) cc_final: 0.8500 (m-30) REVERT: B 257 MET cc_start: 0.9021 (mmp) cc_final: 0.8785 (mmm) REVERT: B 267 MET cc_start: 0.8844 (ttm) cc_final: 0.7919 (mtp) REVERT: B 328 GLU cc_start: 0.9218 (mp0) cc_final: 0.8995 (mp0) REVERT: C 359 LEU cc_start: 0.9132 (tt) cc_final: 0.8926 (mt) REVERT: C 360 GLU cc_start: 0.9122 (pm20) cc_final: 0.8804 (tp30) REVERT: C 391 MET cc_start: 0.3468 (tpt) cc_final: 0.3255 (tpp) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.0841 time to fit residues: 22.7608 Evaluate side-chains 145 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 40.0000 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 151 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 chunk 126 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.193390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.113989 restraints weight = 35129.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 96)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.103468 restraints weight = 28054.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.103180 restraints weight = 20207.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.103350 restraints weight = 16728.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.103365 restraints weight = 15264.167| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12563 Z= 0.177 Angle : 0.863 29.812 17023 Z= 0.393 Chirality : 0.046 0.174 1887 Planarity : 0.005 0.045 2202 Dihedral : 9.237 167.320 1720 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1531 helix: 0.49 (0.20), residues: 668 sheet: 0.25 (0.37), residues: 236 loop : -1.11 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.021 0.002 TYR A 24 PHE 0.033 0.002 PHE B 212 TRP 0.043 0.002 TRP A 21 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00376 (12563) covalent geometry : angle 0.86260 (17023) hydrogen bonds : bond 0.03848 ( 599) hydrogen bonds : angle 5.02242 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7422 (t80) cc_final: 0.7056 (t80) REVERT: A 116 ASP cc_start: 0.9064 (p0) cc_final: 0.8825 (p0) REVERT: A 199 ASP cc_start: 0.9046 (m-30) cc_final: 0.8736 (m-30) REVERT: A 286 LEU cc_start: 0.9094 (mm) cc_final: 0.8806 (mm) REVERT: A 313 MET cc_start: 0.9074 (mpp) cc_final: 0.8147 (mpp) REVERT: A 358 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7826 (tp-100) REVERT: B 37 HIS cc_start: 0.8981 (m-70) cc_final: 0.8653 (m-70) REVERT: B 73 MET cc_start: 0.9461 (mpp) cc_final: 0.8163 (mpp) REVERT: B 83 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.9068 (pp30) REVERT: B 224 ASP cc_start: 0.8847 (m-30) cc_final: 0.8632 (m-30) REVERT: B 267 MET cc_start: 0.8857 (ttm) cc_final: 0.7812 (mtp) REVERT: B 328 GLU cc_start: 0.9259 (mp0) cc_final: 0.9002 (mp0) REVERT: C 352 PHE cc_start: 0.6639 (m-10) cc_final: 0.6388 (m-80) REVERT: C 402 PHE cc_start: 0.5046 (m-10) cc_final: 0.4436 (m-80) REVERT: C 412 PHE cc_start: 0.7667 (t80) cc_final: 0.7380 (t80) REVERT: C 414 MET cc_start: 0.1200 (pmm) cc_final: 0.0929 (pmm) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.0855 time to fit residues: 24.1217 Evaluate side-chains 151 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 overall best weight: 7.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.191861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.119747 restraints weight = 33594.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112179 restraints weight = 29488.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.111507 restraints weight = 21164.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.111281 restraints weight = 16479.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.111309 restraints weight = 15580.373| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12563 Z= 0.176 Angle : 0.856 29.833 17023 Z= 0.390 Chirality : 0.046 0.172 1887 Planarity : 0.005 0.046 2202 Dihedral : 9.183 165.657 1720 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.07 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1531 helix: 0.56 (0.20), residues: 671 sheet: 0.30 (0.37), residues: 234 loop : -1.16 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.023 0.002 TYR B 106 PHE 0.018 0.002 PHE A 418 TRP 0.050 0.002 TRP A 21 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00375 (12563) covalent geometry : angle 0.85638 (17023) hydrogen bonds : bond 0.03802 ( 599) hydrogen bonds : angle 4.92215 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7548 (t80) cc_final: 0.7176 (t80) REVERT: A 116 ASP cc_start: 0.9036 (p0) cc_final: 0.8771 (p0) REVERT: A 199 ASP cc_start: 0.8957 (m-30) cc_final: 0.8694 (m-30) REVERT: A 286 LEU cc_start: 0.8901 (mm) cc_final: 0.8686 (mm) REVERT: A 313 MET cc_start: 0.9039 (mpp) cc_final: 0.8131 (mpp) REVERT: A 358 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7766 (tp-100) REVERT: B 37 HIS cc_start: 0.8874 (m-70) cc_final: 0.8606 (m-70) REVERT: B 73 MET cc_start: 0.9359 (mpp) cc_final: 0.8221 (mpp) REVERT: B 267 MET cc_start: 0.8768 (ttm) cc_final: 0.7806 (mtp) REVERT: B 403 MET cc_start: 0.8039 (mmm) cc_final: 0.7120 (mtm) REVERT: C 398 PHE cc_start: 0.5693 (m-10) cc_final: 0.5482 (m-10) REVERT: C 643 MET cc_start: -0.3463 (mmp) cc_final: -0.3797 (mmp) REVERT: C 663 PHE cc_start: 0.3019 (m-10) cc_final: 0.2717 (m-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0887 time to fit residues: 24.4948 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 122 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 249 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN D 629 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.196936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.131201 restraints weight = 35018.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121259 restraints weight = 27956.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.120705 restraints weight = 17979.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.120970 restraints weight = 13646.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.120949 restraints weight = 11361.024| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12563 Z= 0.127 Angle : 0.840 29.926 17023 Z= 0.378 Chirality : 0.046 0.174 1887 Planarity : 0.005 0.045 2202 Dihedral : 9.060 166.306 1720 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1531 helix: 0.77 (0.20), residues: 662 sheet: 0.89 (0.39), residues: 206 loop : -1.19 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.015 0.001 TYR B 106 PHE 0.023 0.002 PHE A 418 TRP 0.034 0.002 TRP A 21 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00269 (12563) covalent geometry : angle 0.84019 (17023) hydrogen bonds : bond 0.03608 ( 599) hydrogen bonds : angle 4.79836 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7361 (t80) cc_final: 0.6920 (t80) REVERT: A 116 ASP cc_start: 0.9002 (p0) cc_final: 0.8793 (p0) REVERT: A 169 PHE cc_start: 0.8439 (t80) cc_final: 0.7519 (t80) REVERT: A 313 MET cc_start: 0.9087 (mpp) cc_final: 0.8240 (mpp) REVERT: A 358 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7773 (tp-100) REVERT: B 37 HIS cc_start: 0.8900 (m-70) cc_final: 0.8623 (m-70) REVERT: B 45 ASP cc_start: 0.8981 (t70) cc_final: 0.8655 (m-30) REVERT: B 73 MET cc_start: 0.9411 (mpp) cc_final: 0.8137 (mpp) REVERT: B 134 GLN cc_start: 0.8777 (pm20) cc_final: 0.8550 (pm20) REVERT: B 224 ASP cc_start: 0.8978 (m-30) cc_final: 0.8742 (m-30) REVERT: B 267 MET cc_start: 0.8773 (ttm) cc_final: 0.8155 (ttt) REVERT: B 300 MET cc_start: 0.8274 (tpp) cc_final: 0.7965 (tpp) REVERT: B 328 GLU cc_start: 0.9427 (mp0) cc_final: 0.9073 (mp0) REVERT: B 403 MET cc_start: 0.7840 (mmm) cc_final: 0.6966 (mtt) REVERT: C 360 GLU cc_start: 0.9083 (pm20) cc_final: 0.8819 (tp30) REVERT: C 412 PHE cc_start: 0.7957 (t80) cc_final: 0.7584 (t80) REVERT: C 663 PHE cc_start: 0.2945 (m-10) cc_final: 0.2657 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0824 time to fit residues: 24.4448 Evaluate side-chains 153 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 119 optimal weight: 50.0000 chunk 112 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 85 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.194063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.123202 restraints weight = 33398.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.115519 restraints weight = 24564.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.115197 restraints weight = 17015.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.113531 restraints weight = 14807.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.112841 restraints weight = 14041.151| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12563 Z= 0.143 Angle : 0.840 29.883 17023 Z= 0.379 Chirality : 0.045 0.192 1887 Planarity : 0.004 0.046 2202 Dihedral : 9.017 164.468 1720 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.22), residues: 1531 helix: 0.78 (0.20), residues: 667 sheet: 0.35 (0.37), residues: 232 loop : -1.19 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.015 0.001 TYR B 106 PHE 0.027 0.002 PHE B 20 TRP 0.054 0.002 TRP A 21 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00312 (12563) covalent geometry : angle 0.84017 (17023) hydrogen bonds : bond 0.03609 ( 599) hydrogen bonds : angle 4.75397 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7571 (t80) cc_final: 0.7128 (t80) REVERT: A 116 ASP cc_start: 0.9035 (p0) cc_final: 0.8830 (p0) REVERT: A 169 PHE cc_start: 0.8465 (t80) cc_final: 0.8213 (t80) REVERT: A 286 LEU cc_start: 0.9101 (mm) cc_final: 0.8871 (mm) REVERT: A 313 MET cc_start: 0.8853 (mpp) cc_final: 0.7961 (mpp) REVERT: A 316 CYS cc_start: 0.8962 (t) cc_final: 0.8718 (t) REVERT: A 358 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7865 (tp-100) REVERT: B 37 HIS cc_start: 0.8900 (m-70) cc_final: 0.8643 (m-70) REVERT: B 45 ASP cc_start: 0.9017 (t70) cc_final: 0.8692 (m-30) REVERT: B 73 MET cc_start: 0.9376 (mpp) cc_final: 0.8278 (mpp) REVERT: B 224 ASP cc_start: 0.8980 (m-30) cc_final: 0.8740 (m-30) REVERT: B 267 MET cc_start: 0.8838 (ttm) cc_final: 0.7693 (mtp) REVERT: B 328 GLU cc_start: 0.9374 (mp0) cc_final: 0.9038 (mp0) REVERT: B 403 MET cc_start: 0.8068 (mmm) cc_final: 0.7107 (mtm) REVERT: C 398 PHE cc_start: 0.4776 (m-10) cc_final: 0.4555 (m-10) REVERT: C 412 PHE cc_start: 0.7588 (t80) cc_final: 0.7267 (t80) REVERT: C 663 PHE cc_start: 0.2707 (m-10) cc_final: 0.2446 (m-80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0986 time to fit residues: 27.5348 Evaluate side-chains 154 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.205776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.078572 restraints weight = 51319.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.077649 restraints weight = 39848.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.078042 restraints weight = 36305.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.077910 restraints weight = 34677.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.077910 restraints weight = 34430.405| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12563 Z= 0.204 Angle : 0.882 29.857 17023 Z= 0.404 Chirality : 0.046 0.190 1887 Planarity : 0.005 0.047 2202 Dihedral : 9.200 164.043 1720 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1531 helix: 0.74 (0.20), residues: 661 sheet: 0.82 (0.39), residues: 215 loop : -1.29 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.027 0.002 TYR B 281 PHE 0.032 0.002 PHE B 20 TRP 0.076 0.003 TRP A 21 HIS 0.007 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00437 (12563) covalent geometry : angle 0.88171 (17023) hydrogen bonds : bond 0.03888 ( 599) hydrogen bonds : angle 4.86678 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.69 seconds wall clock time: 89 minutes 13.41 seconds (5353.41 seconds total)