Starting phenix.real_space_refine on Tue May 5 03:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbn_61320/05_2026/9jbn_61320.map" } resolution = 2.3 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= -0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 C 8007 2.51 5 N 2146 2.21 5 O 2629 1.98 5 H 12516 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25358 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9916 Classifications: {'peptide': 616} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 593} Chain: "B" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 8269 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 501} Chain: "C" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6863 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 401} Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 202 Unusual residues: {'AMP%rna2p': 1, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1, 'water': 166} Modifications used: {'rna2p': 1} Link IDs: {None: 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 4.64, per 1000 atoms: 0.18 Number of scatterers: 25358 At special positions: 0 Unit cell: (112.32, 144.96, 111.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 2 15.00 O 2629 8.00 N 2146 7.00 C 8007 6.00 H 12516 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 668.5 milliseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 7 sheets defined 57.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 98 through 101 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 123 through 140 removed outlier: 3.693A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.723A pdb=" N MET A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.640A pdb=" N VAL A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.619A pdb=" N THR A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.814A pdb=" N ILE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 351 through 380 removed outlier: 3.863A pdb=" N GLU A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.981A pdb=" N LYS A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 415 through 441 removed outlier: 3.588A pdb=" N VAL A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 451 through 476 Proline residue: A 467 - end of helix removed outlier: 3.582A pdb=" N HIS A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.795A pdb=" N ILE A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 529 through 537 Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.617A pdb=" N VAL A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.841A pdb=" N HIS A 609 " --> pdb=" O ASN A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.606A pdb=" N ALA B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.388A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.531A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 207 through 221 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.528A pdb=" N GLU B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS B 229 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 230 " --> pdb=" O GLU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.713A pdb=" N LEU B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.637A pdb=" N VAL B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 326 removed outlier: 4.297A pdb=" N ALA B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Proline residue: B 312 - end of helix Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 342 through 368 removed outlier: 4.224A pdb=" N PHE B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 378 through 403 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.860A pdb=" N GLU B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 471 through 495 Proline residue: B 484 - end of helix Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 507 through 524 Processing helix chain 'C' and resid 390 through 405 removed outlier: 4.205A pdb=" N ALA C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.670A pdb=" N LEU C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 483 through 495 Processing helix chain 'C' and resid 515 through 521 removed outlier: 3.983A pdb=" N GLU C 519 " --> pdb=" O PRO C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.860A pdb=" N TRP C 543 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.712A pdb=" N ILE C 569 " --> pdb=" O PRO C 566 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 570 " --> pdb=" O PRO C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 599 removed outlier: 3.813A pdb=" N ILE C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 650 removed outlier: 4.198A pdb=" N ILE C 649 " --> pdb=" O ASP C 645 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 650 " --> pdb=" O ILE C 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 645 through 650' Processing helix chain 'C' and resid 668 through 674 removed outlier: 3.706A pdb=" N CYS C 672 " --> pdb=" O SER C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 698 Processing helix chain 'C' and resid 716 through 722 removed outlier: 3.747A pdb=" N CYS C 720 " --> pdb=" O VAL C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 746 removed outlier: 3.549A pdb=" N VAL C 746 " --> pdb=" O ILE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 769 removed outlier: 3.551A pdb=" N VAL C 766 " --> pdb=" O PRO C 763 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 767 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 784 removed outlier: 4.059A pdb=" N LEU C 782 " --> pdb=" O ARG C 779 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP C 783 " --> pdb=" O GLU C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 806 through 810 removed outlier: 3.599A pdb=" N LEU C 809 " --> pdb=" O ARG C 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 4.660A pdb=" N HIS A 122 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS A 153 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 182 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 155 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N SER A 184 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 179 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 274 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN A 181 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER A 276 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 183 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 43 removed outlier: 4.078A pdb=" N HIS B 117 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 116 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N CYS B 171 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS B 144 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 173 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 146 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER B 175 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 170 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU B 195 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS B 172 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N CYS B 197 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 174 " --> pdb=" O CYS B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 64 Processing sheet with id=AA5, first strand: chain 'C' and resid 427 through 428 Processing sheet with id=AA6, first strand: chain 'C' and resid 504 through 506 removed outlier: 6.408A pdb=" N VAL C 531 " --> pdb=" O ILE C 555 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS C 557 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 533 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 554 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE C 581 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 556 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 605 " --> pdb=" O SER C 629 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE C 631 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 607 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 628 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP C 659 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 630 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 680 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 704 " --> pdb=" O ASP C 729 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 728 " --> pdb=" O ASP C 753 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 752 " --> pdb=" O ILE C 776 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 775 " --> pdb=" O GLU C 798 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 562 through 564 595 hydrogen bonds defined for protein. 1668 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: 5.58 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12487 1.03 - 1.23: 67 1.23 - 1.42: 5343 1.42 - 1.62: 7376 1.62 - 1.81: 87 Bond restraints: 25360 Sorted by residual: bond pdb=" O5 RP5 A 702 " pdb=" P' RP5 A 702 " ideal model delta sigma weight residual 1.722 1.609 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C4 AMP A 701 " pdb=" C5 AMP A 701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C5 AMP A 701 " pdb=" C6 AMP A 701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C ILE C 533 " pdb=" O ILE C 533 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.07e-02 8.73e+03 1.53e+01 bond pdb=" CA THR C 535 " pdb=" C THR C 535 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.34e-02 5.57e+03 8.12e+00 ... (remaining 25355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 45522 2.06 - 4.13: 313 4.13 - 6.19: 23 6.19 - 8.26: 5 8.26 - 10.32: 5 Bond angle restraints: 45868 Sorted by residual: angle pdb=" N ARG C 510 " pdb=" CA ARG C 510 " pdb=" CB ARG C 510 " ideal model delta sigma weight residual 109.85 119.01 -9.16 1.49e+00 4.50e-01 3.78e+01 angle pdb=" C ARG C 510 " pdb=" CA ARG C 510 " pdb=" CB ARG C 510 " ideal model delta sigma weight residual 109.89 101.91 7.98 1.60e+00 3.91e-01 2.49e+01 angle pdb=" CA ILE C 533 " pdb=" C ILE C 533 " pdb=" O ILE C 533 " ideal model delta sigma weight residual 120.39 115.88 4.51 1.05e+00 9.07e-01 1.85e+01 angle pdb=" N ARG A 29 " pdb=" CA ARG A 29 " pdb=" CB ARG A 29 " ideal model delta sigma weight residual 114.17 110.21 3.96 1.14e+00 7.69e-01 1.21e+01 angle pdb=" C1' AMP A 701 " pdb=" C2' AMP A 701 " pdb=" C3' AMP A 701 " ideal model delta sigma weight residual 111.00 100.68 10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 45863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.25: 11032 24.25 - 48.51: 687 48.51 - 72.76: 159 72.76 - 97.02: 26 97.02 - 121.27: 1 Dihedral angle restraints: 11905 sinusoidal: 6481 harmonic: 5424 Sorted by residual: dihedral pdb=" C5' AMP A 701 " pdb=" O5' AMP A 701 " pdb=" P AMP A 701 " pdb=" O3P AMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 61.27 -121.27 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" CA LEU B 391 " pdb=" C LEU B 391 " pdb=" N ALA B 392 " pdb=" CA ALA B 392 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLU A 587 " pdb=" C GLU A 587 " pdb=" N ILE A 588 " pdb=" CA ILE A 588 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 11902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1659 0.054 - 0.109: 219 0.109 - 0.163: 54 0.163 - 0.217: 1 0.217 - 0.271: 2 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C2 RP5 A 702 " pdb=" C1 RP5 A 702 " pdb=" C3 RP5 A 702 " pdb=" O2 RP5 A 702 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' AMP A 701 " pdb=" C2' AMP A 701 " pdb=" C4' AMP A 701 " pdb=" O3' AMP A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE C 533 " pdb=" N ILE C 533 " pdb=" C ILE C 533 " pdb=" CB ILE C 533 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 1932 not shown) Planarity restraints: 3714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 510 " 0.952 9.50e-02 1.11e+02 4.87e-01 3.17e+03 pdb=" NE ARG C 510 " 0.406 2.00e-02 2.50e+03 pdb=" CZ ARG C 510 " 0.103 2.00e-02 2.50e+03 pdb=" NH1 ARG C 510 " -0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG C 510 " -0.050 2.00e-02 2.50e+03 pdb="HH11 ARG C 510 " 0.435 2.00e-02 2.50e+03 pdb="HH12 ARG C 510 " -0.669 2.00e-02 2.50e+03 pdb="HH21 ARG C 510 " 0.338 2.00e-02 2.50e+03 pdb="HH22 ARG C 510 " -0.542 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 509 " -0.011 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" N ARG C 510 " 0.035 2.00e-02 2.50e+03 pdb=" CA ARG C 510 " -0.009 2.00e-02 2.50e+03 pdb=" H ARG C 510 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 533 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ILE C 533 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE C 533 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 534 " -0.011 2.00e-02 2.50e+03 ... (remaining 3711 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1825 2.21 - 2.81: 50885 2.81 - 3.40: 65493 3.40 - 4.00: 89836 4.00 - 4.60: 138627 Nonbonded interactions: 346666 Sorted by model distance: nonbonded pdb=" OE1 GLU C 517 " pdb=" H GLU C 517 " model vdw 1.612 2.450 nonbonded pdb=" HZ2 LYS A 440 " pdb=" O HOH A 809 " model vdw 1.627 2.450 nonbonded pdb="HH11 ARG A 196 " pdb=" O HOH A 812 " model vdw 1.638 2.450 nonbonded pdb="HE21 GLN B 389 " pdb=" O HOH B 606 " model vdw 1.642 2.450 nonbonded pdb="HE21 GLN A 356 " pdb=" O HOH A 815 " model vdw 1.646 2.450 ... (remaining 346661 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 0.113 12845 Z= 0.210 Angle : 0.650 10.325 17384 Z= 0.356 Chirality : 0.042 0.271 1935 Planarity : 0.006 0.147 2219 Dihedral : 18.062 121.270 4807 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % Rotamer: Outliers : 1.08 % Allowed : 21.24 % Favored : 77.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.59 % 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 (0.21), residues: 1555 helix: 0.87 (0.19), residues: 788 sheet: 0.16 (0.39), residues: 147 loop : -0.51 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.017 0.002 TYR A 406 PHE 0.015 0.002 PHE A 166 TRP 0.013 0.002 TRP B 381 HIS 0.005 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00431 (12844) covalent geometry : angle 0.65011 (17384) hydrogen bonds : bond 0.16045 ( 595) hydrogen bonds : angle 5.16506 ( 1668) Misc. bond : bond 0.01343 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.7741 (tt0) cc_final: 0.7375 (tt0) REVERT: B 141 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8058 (mmt90) REVERT: B 311 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8066 (mm) REVERT: B 497 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 572 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7345 (mtt) outliers start: 15 outliers final: 12 residues processed: 141 average time/residue: 1.8146 time to fit residues: 272.5672 Evaluate side-chains 137 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 690 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 522 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.151966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117673 restraints weight = 40930.401| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.17 r_work: 0.3380 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12845 Z= 0.155 Angle : 0.571 7.364 17384 Z= 0.307 Chirality : 0.041 0.157 1935 Planarity : 0.005 0.040 2219 Dihedral : 6.477 67.496 1751 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.04 % Rotamer: Outliers : 2.09 % Allowed : 19.87 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.35 (0.21), residues: 1555 helix: 0.84 (0.19), residues: 808 sheet: 0.21 (0.40), residues: 143 loop : -0.47 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 510 TYR 0.015 0.002 TYR A 406 PHE 0.015 0.002 PHE A 166 TRP 0.012 0.002 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00339 (12844) covalent geometry : angle 0.57141 (17384) hydrogen bonds : bond 0.07466 ( 595) hydrogen bonds : angle 4.54222 ( 1668) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 256 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: B 80 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: B 103 GLU cc_start: 0.7753 (tt0) cc_final: 0.7381 (tt0) REVERT: B 141 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8025 (mmt90) REVERT: B 311 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7925 (mm) REVERT: B 364 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7128 (ttpp) REVERT: B 497 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: C 458 ASN cc_start: 0.7714 (m-40) cc_final: 0.7278 (t0) REVERT: C 540 GLN cc_start: 0.7853 (tp40) cc_final: 0.7548 (tp-100) outliers start: 29 outliers final: 12 residues processed: 157 average time/residue: 1.7042 time to fit residues: 286.1030 Evaluate side-chains 144 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 690 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119276 restraints weight = 40690.203| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.18 r_work: 0.3404 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12845 Z= 0.123 Angle : 0.519 6.771 17384 Z= 0.276 Chirality : 0.039 0.149 1935 Planarity : 0.004 0.043 2219 Dihedral : 5.822 55.998 1739 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 2.23 % Allowed : 19.65 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.61 (0.21), residues: 1555 helix: 1.12 (0.19), residues: 805 sheet: 0.28 (0.41), residues: 142 loop : -0.44 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.014 0.002 TYR A 406 PHE 0.014 0.001 PHE C 397 TRP 0.010 0.001 TRP B 26 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00260 (12844) covalent geometry : angle 0.51865 (17384) hydrogen bonds : bond 0.06315 ( 595) hydrogen bonds : angle 4.32443 ( 1668) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: B 141 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8046 (mmt90) REVERT: B 311 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 329 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: B 364 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7115 (ttpp) REVERT: B 429 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6706 (mttt) REVERT: B 497 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: C 430 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: C 458 ASN cc_start: 0.7690 (m-40) cc_final: 0.7337 (t0) REVERT: C 655 ASP cc_start: 0.8158 (t0) cc_final: 0.7902 (t0) outliers start: 31 outliers final: 11 residues processed: 148 average time/residue: 1.7163 time to fit residues: 271.4905 Evaluate side-chains 137 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 632 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117966 restraints weight = 40647.830| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.11 r_work: 0.3380 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12845 Z= 0.155 Angle : 0.550 7.562 17384 Z= 0.294 Chirality : 0.041 0.162 1935 Planarity : 0.005 0.043 2219 Dihedral : 5.586 56.647 1733 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.78 % Rotamer: Outliers : 2.95 % Allowed : 19.15 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.46 (0.21), residues: 1555 helix: 0.99 (0.19), residues: 810 sheet: 0.15 (0.41), residues: 143 loop : -0.49 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.013 0.002 TYR A 473 PHE 0.016 0.002 PHE A 166 TRP 0.012 0.001 TRP B 381 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00346 (12844) covalent geometry : angle 0.55044 (17384) hydrogen bonds : bond 0.07095 ( 595) hydrogen bonds : angle 4.33314 ( 1668) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 256 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: B 94 LEU cc_start: 0.7701 (mm) cc_final: 0.7447 (mt) REVERT: B 141 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8056 (mmt90) REVERT: B 311 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8046 (mm) REVERT: B 364 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7231 (tppp) REVERT: B 497 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 500 LEU cc_start: 0.7810 (mt) cc_final: 0.7323 (pt) REVERT: C 430 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: C 443 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5686 (mp0) REVERT: C 458 ASN cc_start: 0.7668 (m-40) cc_final: 0.7396 (t0) REVERT: C 655 ASP cc_start: 0.8152 (t0) cc_final: 0.7905 (t0) REVERT: C 786 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6882 (mt-10) outliers start: 41 outliers final: 16 residues processed: 151 average time/residue: 1.6709 time to fit residues: 270.5394 Evaluate side-chains 142 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 632 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116077 restraints weight = 40659.467| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.08 r_work: 0.3368 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12845 Z= 0.186 Angle : 0.590 7.823 17384 Z= 0.317 Chirality : 0.042 0.172 1935 Planarity : 0.005 0.043 2219 Dihedral : 5.682 57.609 1733 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 3.02 % Allowed : 19.37 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.24 (0.21), residues: 1555 helix: 0.77 (0.19), residues: 810 sheet: 0.26 (0.40), residues: 140 loop : -0.60 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 475 TYR 0.016 0.002 TYR A 406 PHE 0.016 0.002 PHE A 166 TRP 0.013 0.002 TRP B 381 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00428 (12844) covalent geometry : angle 0.58982 (17384) hydrogen bonds : bond 0.07905 ( 595) hydrogen bonds : angle 4.44786 ( 1668) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 203 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8437 (m) REVERT: A 256 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: B 94 LEU cc_start: 0.7650 (mm) cc_final: 0.7397 (mt) REVERT: B 103 GLU cc_start: 0.7798 (tt0) cc_final: 0.7496 (tt0) REVERT: B 141 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8103 (mmt90) REVERT: B 311 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 364 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7234 (ttpp) REVERT: B 497 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 500 LEU cc_start: 0.7836 (mt) cc_final: 0.7531 (pt) REVERT: C 443 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: C 458 ASN cc_start: 0.7790 (m-40) cc_final: 0.7561 (t0) REVERT: C 655 ASP cc_start: 0.8204 (t0) cc_final: 0.7938 (t0) REVERT: C 786 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6956 (mt-10) outliers start: 42 outliers final: 21 residues processed: 151 average time/residue: 1.7180 time to fit residues: 277.7261 Evaluate side-chains 154 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain C residue 770 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117673 restraints weight = 40916.245| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.08 r_work: 0.3391 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12845 Z= 0.137 Angle : 0.535 7.219 17384 Z= 0.286 Chirality : 0.040 0.153 1935 Planarity : 0.005 0.043 2219 Dihedral : 5.512 58.005 1732 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 2.81 % Allowed : 19.37 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.45 (0.21), residues: 1555 helix: 1.00 (0.19), residues: 809 sheet: 0.26 (0.40), residues: 140 loop : -0.55 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.014 0.002 TYR A 406 PHE 0.014 0.001 PHE A 166 TRP 0.011 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00299 (12844) covalent geometry : angle 0.53482 (17384) hydrogen bonds : bond 0.06685 ( 595) hydrogen bonds : angle 4.29602 ( 1668) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 33 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: A 203 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 256 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: A 386 LYS cc_start: 0.8071 (tptt) cc_final: 0.7841 (mtmp) REVERT: B 7 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 80 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: B 94 LEU cc_start: 0.7754 (mm) cc_final: 0.7509 (mt) REVERT: B 103 GLU cc_start: 0.7746 (tt0) cc_final: 0.7448 (tt0) REVERT: B 141 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8082 (mmt90) REVERT: B 311 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8057 (mm) REVERT: B 329 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 364 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7208 (ttpp) REVERT: B 497 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 500 LEU cc_start: 0.7837 (mt) cc_final: 0.7549 (pt) REVERT: C 443 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.5680 (mp0) REVERT: C 786 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7264 (mt-10) outliers start: 39 outliers final: 21 residues processed: 158 average time/residue: 1.7712 time to fit residues: 299.9282 Evaluate side-chains 156 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 632 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 458 ASN C 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117988 restraints weight = 40799.320| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.10 r_work: 0.3395 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12845 Z= 0.138 Angle : 0.533 7.317 17384 Z= 0.284 Chirality : 0.040 0.157 1935 Planarity : 0.005 0.043 2219 Dihedral : 5.482 58.153 1732 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 2.88 % Allowed : 19.94 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.52 (0.21), residues: 1555 helix: 1.09 (0.19), residues: 803 sheet: 0.24 (0.40), residues: 140 loop : -0.54 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.013 0.002 TYR A 406 PHE 0.014 0.001 PHE A 166 TRP 0.011 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00304 (12844) covalent geometry : angle 0.53275 (17384) hydrogen bonds : bond 0.06584 ( 595) hydrogen bonds : angle 4.24150 ( 1668) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 203 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8325 (m) REVERT: A 256 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: A 386 LYS cc_start: 0.8063 (tptt) cc_final: 0.7843 (mtmp) REVERT: B 7 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: B 94 LEU cc_start: 0.7748 (mm) cc_final: 0.7510 (mt) REVERT: B 103 GLU cc_start: 0.7752 (tt0) cc_final: 0.7457 (mt-10) REVERT: B 141 ARG cc_start: 0.8377 (mmm160) cc_final: 0.8094 (mmt90) REVERT: B 311 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 329 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: B 364 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7288 (tppp) REVERT: B 497 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: B 500 LEU cc_start: 0.7835 (mt) cc_final: 0.7562 (pt) REVERT: C 430 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: C 443 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: C 786 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7294 (mt-10) outliers start: 40 outliers final: 21 residues processed: 153 average time/residue: 1.7098 time to fit residues: 280.8825 Evaluate side-chains 152 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain C residue 770 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117576 restraints weight = 40970.923| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.12 r_work: 0.3383 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12845 Z= 0.151 Angle : 0.546 7.500 17384 Z= 0.292 Chirality : 0.040 0.161 1935 Planarity : 0.005 0.042 2219 Dihedral : 5.530 58.385 1732 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 2.81 % Allowed : 20.09 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.49 (0.21), residues: 1555 helix: 1.05 (0.19), residues: 803 sheet: 0.23 (0.40), residues: 140 loop : -0.54 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.014 0.002 TYR A 406 PHE 0.015 0.002 PHE A 166 TRP 0.012 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00339 (12844) covalent geometry : angle 0.54561 (17384) hydrogen bonds : bond 0.06891 ( 595) hydrogen bonds : angle 4.26225 ( 1668) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 203 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 256 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: A 386 LYS cc_start: 0.8064 (tptt) cc_final: 0.7826 (mtmp) REVERT: B 7 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: B 80 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: B 94 LEU cc_start: 0.7730 (mm) cc_final: 0.7475 (mt) REVERT: B 103 GLU cc_start: 0.7761 (tt0) cc_final: 0.7478 (mt-10) REVERT: B 141 ARG cc_start: 0.8386 (mmm160) cc_final: 0.8102 (mmt90) REVERT: B 311 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 364 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7284 (tppp) REVERT: B 497 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 500 LEU cc_start: 0.7803 (mt) cc_final: 0.7569 (pt) REVERT: C 443 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5605 (mp0) REVERT: C 511 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7150 (mm-30) REVERT: C 786 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7314 (mt-10) outliers start: 39 outliers final: 23 residues processed: 155 average time/residue: 1.6208 time to fit residues: 269.6372 Evaluate side-chains 159 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 632 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 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 = 0.3936 r_free = 0.3936 target = 0.153946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119767 restraints weight = 40798.074| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.11 r_work: 0.3421 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12845 Z= 0.109 Angle : 0.495 6.530 17384 Z= 0.262 Chirality : 0.039 0.145 1935 Planarity : 0.004 0.042 2219 Dihedral : 5.342 58.056 1732 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 20.88 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.79 (0.22), residues: 1555 helix: 1.36 (0.19), residues: 800 sheet: 0.15 (0.40), residues: 145 loop : -0.42 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 724 TYR 0.012 0.001 TYR A 320 PHE 0.011 0.001 PHE A 166 TRP 0.012 0.001 TRP B 26 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00227 (12844) covalent geometry : angle 0.49515 (17384) hydrogen bonds : bond 0.05480 ( 595) hydrogen bonds : angle 4.08463 ( 1668) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 203 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8233 (m) REVERT: A 256 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: A 386 LYS cc_start: 0.8021 (tptt) cc_final: 0.7775 (mtmp) REVERT: B 7 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: B 94 LEU cc_start: 0.7706 (mm) cc_final: 0.7451 (mt) REVERT: B 103 GLU cc_start: 0.7737 (tt0) cc_final: 0.7463 (mt-10) REVERT: B 141 ARG cc_start: 0.8307 (mmm160) cc_final: 0.8029 (mmt90) REVERT: B 268 GLU cc_start: 0.7642 (tt0) cc_final: 0.7310 (tt0) REVERT: B 311 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 364 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7077 (tppp) REVERT: B 497 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 500 LEU cc_start: 0.7773 (mt) cc_final: 0.7560 (pt) REVERT: C 430 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: C 443 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5490 (mp0) REVERT: C 773 ARG cc_start: 0.7409 (mmt-90) cc_final: 0.7098 (ptp90) REVERT: C 786 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7265 (mt-10) outliers start: 27 outliers final: 15 residues processed: 151 average time/residue: 1.5764 time to fit residues: 256.3218 Evaluate side-chains 149 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 690 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 0.0980 chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** C 458 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 = 0.3922 r_free = 0.3922 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118605 restraints weight = 40763.080| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.16 r_work: 0.3389 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12845 Z= 0.134 Angle : 0.525 7.364 17384 Z= 0.278 Chirality : 0.040 0.160 1935 Planarity : 0.004 0.041 2219 Dihedral : 5.414 58.278 1732 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.78 % Rotamer: Outliers : 1.73 % Allowed : 21.02 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.73 (0.22), residues: 1555 helix: 1.28 (0.19), residues: 801 sheet: 0.20 (0.40), residues: 142 loop : -0.43 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.002 TYR A 406 PHE 0.014 0.001 PHE A 166 TRP 0.011 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00296 (12844) covalent geometry : angle 0.52465 (17384) hydrogen bonds : bond 0.06272 ( 595) hydrogen bonds : angle 4.13072 ( 1668) Misc. bond : bond 0.00038 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 203 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8221 (m) REVERT: A 256 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 386 LYS cc_start: 0.8040 (tptt) cc_final: 0.7786 (mtmp) REVERT: B 7 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: B 94 LEU cc_start: 0.7686 (mm) cc_final: 0.7452 (mt) REVERT: B 103 GLU cc_start: 0.7768 (tt0) cc_final: 0.7476 (mt-10) REVERT: B 141 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8048 (mmt90) REVERT: B 311 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8041 (mm) REVERT: B 364 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7123 (tppp) REVERT: B 497 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 500 LEU cc_start: 0.7788 (mt) cc_final: 0.7562 (pt) REVERT: C 430 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: C 443 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5496 (mp0) REVERT: C 511 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7198 (mm-30) REVERT: C 786 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7282 (mt-10) outliers start: 24 outliers final: 15 residues processed: 146 average time/residue: 1.6787 time to fit residues: 262.5640 Evaluate side-chains 149 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 690 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** C 458 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 = 0.3916 r_free = 0.3916 target = 0.152104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117560 restraints weight = 40788.694| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.13 r_work: 0.3379 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12845 Z= 0.143 Angle : 0.536 7.392 17384 Z= 0.285 Chirality : 0.040 0.159 1935 Planarity : 0.005 0.041 2219 Dihedral : 5.460 58.494 1732 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.78 % Rotamer: Outliers : 2.02 % Allowed : 20.81 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.67 (0.21), residues: 1555 helix: 1.22 (0.19), residues: 797 sheet: 0.20 (0.40), residues: 142 loop : -0.43 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 163 TYR 0.014 0.002 TYR A 320 PHE 0.015 0.002 PHE A 166 TRP 0.011 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00320 (12844) covalent geometry : angle 0.53601 (17384) hydrogen bonds : bond 0.06587 ( 595) hydrogen bonds : angle 4.18206 ( 1668) Misc. bond : bond 0.00043 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10679.38 seconds wall clock time: 180 minutes 50.02 seconds (10850.02 seconds total)