Starting phenix.real_space_refine on Sat Aug 8 05:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbn_61320/08_2026/9jbn_61320_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbn_61320/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbn_61320/08_2026/9jbn_61320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbn_61320/08_2026/9jbn_61320.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbn_61320/08_2026/9jbn_61320_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbn_61320/08_2026/9jbn_61320_trim.cif" } 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-2.2rc3-6140/lib/python3.11/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: 3.10, per 1000 atoms: 0.12 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: 2.08 Conformation dependent library (CDL) restraints added in 776.5 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: 5.52 Time building geometry restraints manager: 2.81 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 - 1.85: 45401 1.85 - 3.70: 421 3.70 - 5.55: 37 5.55 - 7.40: 3 7.40 - 9.25: 6 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=" N1 AMP A 701 " pdb=" C2 AMP A 701 " pdb=" N3 AMP A 701 " ideal model delta sigma weight residual 120.00 129.25 -9.25 3.00e+00 1.11e-01 9.51e+00 ... (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: 1661 0.054 - 0.109: 218 0.109 - 0.163: 54 0.163 - 0.217: 1 0.217 - 0.271: 1 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=" 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 chirality pdb=" CB ILE C 533 " pdb=" CA ILE C 533 " pdb=" CG1 ILE C 533 " pdb=" CG2 ILE C 533 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.59e-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: 2.160 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: 0.120 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.370 Find NCS groups from input model: 0.080 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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= 0.209 Angle : 0.637 9.251 17384 Z= 0.354 Chirality : 0.042 0.271 1935 Planarity : 0.006 0.147 2219 Dihedral : 18.060 121.270 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/Z covalent geometry : bond 0.00428 / 0.21 (12844) covalent geometry : angle 0.63722 / 0.35 (17384) hydrogen bonds : bond 0.16045 / 10.34 ( 595) hydrogen bonds : angle 5.16506 / 3.53 ( 1668) Misc. bond : bond 0.01343 / 0.64 ( 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 : 0.591 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: 1.3898 time to fit residues: 211.1681 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 : 0.671 ------------------------------------------------------------------------------- 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: 3.9990 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... 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 = 0.152024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117399 restraints weight = 40948.151| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.14 r_work: 0.3378 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0503 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 : 0.565 6.446 17384 Z= 0.307 Chirality : 0.041 0.158 1935 Planarity : 0.005 0.039 2219 Dihedral : 6.656 84.741 1751 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.04 % Rotamer: Outliers : 2.02 % Allowed : 19.87 % 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: 0.35 (0.21), residues: 1555 helix: 0.83 (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 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12844) covalent geometry : angle 0.56484 / 0.31 (17384) hydrogen bonds : bond 0.07425 / 4.87 ( 595) hydrogen bonds : angle 4.53789 / 3.11 ( 1668) Misc. bond : bond 0.00034 / 0.02 ( 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 163 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 256 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: B 80 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: B 103 GLU cc_start: 0.7755 (tt0) cc_final: 0.7377 (tt0) REVERT: B 141 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8036 (mmt90) REVERT: B 311 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7938 (mm) REVERT: B 364 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7150 (ttpp) REVERT: B 497 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: C 458 ASN cc_start: 0.7714 (m-40) cc_final: 0.7281 (t0) REVERT: C 540 GLN cc_start: 0.7858 (tp40) cc_final: 0.7553 (tp-100) outliers start: 28 outliers final: 12 residues processed: 157 average time/residue: 1.2770 time to fit residues: 217.0154 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 : 0.667 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.6980 chunk 153 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120429 restraints weight = 40774.348| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.15 r_work: 0.3421 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12845 Z= 0.114 Angle : 0.498 6.776 17384 Z= 0.267 Chirality : 0.039 0.146 1935 Planarity : 0.004 0.042 2219 Dihedral : 5.983 56.711 1739 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.44 % Favored : 97.43 % Rotamer: Outliers : 2.16 % Allowed : 19.73 % 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: 0.70 (0.21), residues: 1555 helix: 1.20 (0.19), residues: 806 sheet: 0.31 (0.41), residues: 142 loop : -0.41 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.012 0.001 TYR A 406 PHE 0.016 0.001 PHE C 397 TRP 0.010 0.001 TRP B 26 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (12844) covalent geometry : angle 0.49840 / 0.27 (17384) hydrogen bonds : bond 0.05899 / 3.87 ( 595) hydrogen bonds : angle 4.25669 / 2.92 ( 1668) Misc. bond : bond 0.00021 / 0.01 ( 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 157 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: B 141 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8028 (mmt90) REVERT: B 311 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (mm) REVERT: B 329 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: B 364 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7013 (ttpp) REVERT: B 429 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6689 (mttt) REVERT: B 497 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: C 430 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8191 (m-30) REVERT: C 458 ASN cc_start: 0.7652 (m-40) cc_final: 0.7326 (t0) REVERT: C 655 ASP cc_start: 0.8120 (t0) cc_final: 0.7867 (t0) outliers start: 30 outliers final: 10 residues processed: 149 average time/residue: 1.3265 time to fit residues: 213.7362 Evaluate side-chains 138 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 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: 4.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120070 restraints weight = 39588.540| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.18 r_work: 0.3542 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12845 Z= 0.124 Angle : 0.503 6.092 17384 Z= 0.270 Chirality : 0.039 0.145 1935 Planarity : 0.004 0.042 2219 Dihedral : 5.628 55.885 1733 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.11 % Rotamer: Outliers : 2.59 % Allowed : 19.29 % 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: 0.72 (0.21), residues: 1555 helix: 1.25 (0.19), residues: 806 sheet: 0.13 (0.41), residues: 145 loop : -0.40 (0.24), residues: 604 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 0.010 0.001 TRP B 381 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12844) covalent geometry : angle 0.50333 / 0.27 (17384) hydrogen bonds : bond 0.06131 / 4.04 ( 595) hydrogen bonds : angle 4.19418 / 2.88 ( 1668) Misc. bond : bond 0.00011 / 0.01 ( 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 164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 33 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: A 256 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: A 386 LYS cc_start: 0.8033 (tptt) cc_final: 0.7709 (mtmt) REVERT: B 141 ARG cc_start: 0.8353 (mmm160) cc_final: 0.8053 (mmt90) REVERT: B 311 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (mm) REVERT: B 329 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: B 364 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7125 (tppp) REVERT: B 429 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6643 (mttt) REVERT: B 497 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 430 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: C 443 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: C 458 ASN cc_start: 0.7645 (m-40) cc_final: 0.7368 (t0) REVERT: C 655 ASP cc_start: 0.8097 (t0) cc_final: 0.7861 (t0) outliers start: 36 outliers final: 15 residues processed: 154 average time/residue: 1.2862 time to fit residues: 214.8045 Evaluate side-chains 146 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 256 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 329 GLU Chi-restraints excluded: chain B residue 338 LYS 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 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 Chi-restraints excluded: chain C residue 811 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN B 386 GLN C 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117071 restraints weight = 39606.510| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.12 r_work: 0.3489 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1026 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= 0.190 Angle : 0.583 6.809 17384 Z= 0.317 Chirality : 0.042 0.150 1935 Planarity : 0.005 0.043 2219 Dihedral : 5.866 58.947 1733 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 2.95 % Allowed : 18.79 % Favored : 78.26 % 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: 0.28 (0.21), residues: 1555 helix: 0.82 (0.19), residues: 810 sheet: 0.12 (0.40), residues: 143 loop : -0.55 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 492 TYR 0.016 0.002 TYR A 473 PHE 0.018 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/Z covalent geometry : bond 0.00437 / 0.19 (12844) covalent geometry : angle 0.58348 / 0.32 (17384) hydrogen bonds : bond 0.08003 / 5.28 ( 595) hydrogen bonds : angle 4.43812 / 3.05 ( 1668) Misc. bond : bond 0.00015 / 0.01 ( 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 164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 203 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8377 (m) REVERT: A 256 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: B 7 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: B 94 LEU cc_start: 0.7542 (mm) cc_final: 0.7267 (mt) REVERT: B 103 GLU cc_start: 0.7778 (tt0) cc_final: 0.7481 (tt0) REVERT: B 141 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8140 (mmt90) REVERT: B 311 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 364 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7157 (ttpp) REVERT: B 497 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: B 500 LEU cc_start: 0.7786 (mt) cc_final: 0.7428 (pt) REVERT: C 443 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.5648 (mp0) REVERT: C 458 ASN cc_start: 0.7784 (m-40) cc_final: 0.7511 (t0) REVERT: C 655 ASP cc_start: 0.8222 (t0) cc_final: 0.7948 (t0) REVERT: C 786 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6905 (mt-10) outliers start: 41 outliers final: 19 residues processed: 150 average time/residue: 1.3847 time to fit residues: 224.5289 Evaluate side-chains 152 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 325 GLN Chi-restraints excluded: chain B residue 7 GLU 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 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 545 ASP Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 632 PHE 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: 3.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4082 r_free = 0.4082 target = 0.155266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.118857 restraints weight = 40008.031| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.15 r_work: 0.3508 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1117 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= 0.138 Angle : 0.521 6.041 17384 Z= 0.282 Chirality : 0.040 0.141 1935 Planarity : 0.005 0.042 2219 Dihedral : 5.771 57.799 1732 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.89 % Favored : 96.98 % Rotamer: Outliers : 2.52 % Allowed : 19.15 % Favored : 78.33 % 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: 0.51 (0.21), residues: 1555 helix: 1.05 (0.19), residues: 804 sheet: 0.19 (0.40), residues: 142 loop : -0.49 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.014 0.002 TYR A 406 PHE 0.014 0.002 PHE A 166 TRP 0.011 0.001 TRP B 381 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12844) covalent geometry : angle 0.52109 / 0.28 (17384) hydrogen bonds : bond 0.06622 / 4.35 ( 595) hydrogen bonds : angle 4.26843 / 2.94 ( 1668) Misc. bond : bond 0.00005 / 0.00 ( 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 164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 33 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: A 203 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8324 (m) REVERT: A 256 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: A 386 LYS cc_start: 0.8058 (tptt) cc_final: 0.7739 (mtmp) REVERT: B 7 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: B 80 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6844 (tp30) REVERT: B 94 LEU cc_start: 0.7645 (mm) cc_final: 0.7384 (mt) REVERT: B 103 GLU cc_start: 0.7748 (tt0) cc_final: 0.7441 (tt0) REVERT: B 141 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8122 (mmt90) REVERT: B 311 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8008 (mm) REVERT: B 364 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7136 (ttpp) REVERT: B 497 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: B 500 LEU cc_start: 0.7793 (mt) cc_final: 0.7449 (pt) REVERT: C 430 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: C 443 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: C 458 ASN cc_start: 0.7771 (m-40) cc_final: 0.7569 (t0) REVERT: C 786 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6926 (mt-10) outliers start: 35 outliers final: 17 residues processed: 155 average time/residue: 1.4386 time to fit residues: 241.2943 Evaluate side-chains 151 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 325 GLN 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 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 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 Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain C residue 787 LYS 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: 0.0470 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.157089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121006 restraints weight = 39735.643| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.14 r_work: 0.3538 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12845 Z= 0.109 Angle : 0.482 6.089 17384 Z= 0.257 Chirality : 0.039 0.144 1935 Planarity : 0.004 0.042 2219 Dihedral : 5.625 57.543 1732 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.11 % Rotamer: Outliers : 2.16 % Allowed : 19.87 % Favored : 77.97 % 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: 0.82 (0.22), residues: 1555 helix: 1.39 (0.19), residues: 801 sheet: 0.15 (0.40), residues: 145 loop : -0.42 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 5 TYR 0.012 0.001 TYR A 320 PHE 0.011 0.001 PHE A 166 TRP 0.011 0.001 TRP B 26 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12844) covalent geometry : angle 0.48230 / 0.26 (17384) hydrogen bonds : bond 0.05430 / 3.57 ( 595) hydrogen bonds : angle 4.07136 / 2.80 ( 1668) Misc. bond : bond 0.00006 / 0.00 ( 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 159 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 203 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 256 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: A 386 LYS cc_start: 0.8019 (tptt) cc_final: 0.7710 (mtmp) REVERT: B 7 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6328 (tm-30) REVERT: B 94 LEU cc_start: 0.7683 (mm) cc_final: 0.7426 (mt) REVERT: B 103 GLU cc_start: 0.7693 (tt0) cc_final: 0.7412 (tt0) REVERT: B 141 ARG cc_start: 0.8328 (mmm160) cc_final: 0.8051 (mmt90) REVERT: B 268 GLU cc_start: 0.7666 (tt0) cc_final: 0.7343 (tt0) REVERT: B 311 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7962 (mm) REVERT: B 329 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: B 364 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7090 (tppp) REVERT: B 429 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6627 (mttt) REVERT: B 497 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 500 LEU cc_start: 0.7758 (mt) cc_final: 0.7466 (pt) REVERT: C 430 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: C 443 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5439 (mp0) REVERT: C 773 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.7081 (ptp90) REVERT: C 786 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7287 (mt-10) outliers start: 30 outliers final: 11 residues processed: 154 average time/residue: 1.4031 time to fit residues: 233.7672 Evaluate side-chains 142 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 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 443 GLU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 632 PHE 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: 5.9990 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN C 458 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120278 restraints weight = 39825.129| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.15 r_work: 0.3531 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12845 Z= 0.120 Angle : 0.495 6.177 17384 Z= 0.265 Chirality : 0.039 0.139 1935 Planarity : 0.004 0.040 2219 Dihedral : 5.589 57.583 1732 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.51 % Favored : 97.36 % Rotamer: Outliers : 2.09 % Allowed : 20.23 % Favored : 77.68 % 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: 0.82 (0.22), residues: 1555 helix: 1.38 (0.19), residues: 801 sheet: 0.16 (0.40), residues: 144 loop : -0.41 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.012 0.002 TYR A 406 PHE 0.013 0.001 PHE A 166 TRP 0.009 0.001 TRP B 381 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12844) covalent geometry : angle 0.49488 / 0.27 (17384) hydrogen bonds : bond 0.05810 / 3.82 ( 595) hydrogen bonds : angle 4.07642 / 2.80 ( 1668) Misc. bond : bond 0.00011 / 0.01 ( 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 154 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 203 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8164 (m) REVERT: A 256 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 386 LYS cc_start: 0.8014 (tptt) cc_final: 0.7713 (mtmp) REVERT: B 7 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6287 (tm-30) REVERT: B 94 LEU cc_start: 0.7625 (mm) cc_final: 0.7372 (mt) REVERT: B 103 GLU cc_start: 0.7684 (tt0) cc_final: 0.7400 (tt0) REVERT: B 110 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7872 (mmpt) REVERT: B 141 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8065 (mmt90) REVERT: B 311 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7974 (mm) REVERT: B 364 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7096 (tppp) REVERT: B 497 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 500 LEU cc_start: 0.7764 (mt) cc_final: 0.7464 (pt) REVERT: C 430 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: C 443 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: C 786 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7279 (mt-10) outliers start: 29 outliers final: 15 residues processed: 148 average time/residue: 1.3443 time to fit residues: 215.8395 Evaluate side-chains 148 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 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 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 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 632 PHE Chi-restraints excluded: chain C residue 690 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 0.0040 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3959 r_free = 0.3959 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121928 restraints weight = 40850.075| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.14 r_work: 0.3440 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1514 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= 0.098 Angle : 0.467 5.922 17384 Z= 0.247 Chirality : 0.038 0.143 1935 Planarity : 0.004 0.039 2219 Dihedral : 5.492 57.214 1732 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.12 % Favored : 97.75 % Rotamer: Outliers : 1.80 % Allowed : 20.59 % 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: 1.08 (0.22), residues: 1555 helix: 1.61 (0.19), residues: 800 sheet: 0.21 (0.40), residues: 143 loop : -0.30 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 773 TYR 0.011 0.001 TYR A 320 PHE 0.010 0.001 PHE A 166 TRP 0.012 0.001 TRP B 26 HIS 0.002 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (12844) covalent geometry : angle 0.46737 / 0.25 (17384) hydrogen bonds : bond 0.04788 / 3.15 ( 595) hydrogen bonds : angle 3.93503 / 2.70 ( 1668) Misc. bond : bond 0.00016 / 0.01 ( 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 157 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 23 GLN cc_start: 0.7607 (mt0) cc_final: 0.7323 (tt0) REVERT: A 203 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8141 (m) REVERT: A 256 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: A 386 LYS cc_start: 0.8034 (tptt) cc_final: 0.7798 (mtmt) REVERT: B 7 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: B 94 LEU cc_start: 0.7749 (mm) cc_final: 0.7504 (mt) REVERT: B 103 GLU cc_start: 0.7667 (tt0) cc_final: 0.7442 (mt-10) REVERT: B 110 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7816 (mmpt) REVERT: B 141 ARG cc_start: 0.8310 (mmm160) cc_final: 0.8040 (mmt90) REVERT: B 268 GLU cc_start: 0.7600 (tt0) cc_final: 0.7229 (tt0) REVERT: B 311 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 364 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7031 (tppp) REVERT: B 429 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6610 (mttt) REVERT: B 497 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 500 LEU cc_start: 0.7785 (mt) cc_final: 0.7575 (pt) REVERT: C 430 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: C 773 ARG cc_start: 0.7395 (mmt-90) cc_final: 0.7073 (ptp90) REVERT: C 786 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7280 (mt-10) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 1.4823 time to fit residues: 242.0957 Evaluate side-chains 144 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 B residue 7 GLU Chi-restraints excluded: chain B residue 42 ASP 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 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 513 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3938 r_free = 0.3938 target = 0.154119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120298 restraints weight = 40701.804| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.17 r_work: 0.3418 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12845 Z= 0.118 Angle : 0.492 6.113 17384 Z= 0.262 Chirality : 0.039 0.164 1935 Planarity : 0.004 0.039 2219 Dihedral : 5.462 57.505 1732 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 1.66 % Allowed : 20.81 % Favored : 77.54 % 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: 0.98 (0.22), residues: 1555 helix: 1.51 (0.19), residues: 801 sheet: 0.17 (0.40), residues: 145 loop : -0.30 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.012 0.001 TYR A 406 PHE 0.013 0.001 PHE A 166 TRP 0.009 0.001 TRP B 381 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12844) covalent geometry : angle 0.49216 / 0.26 (17384) hydrogen bonds : bond 0.05560 / 3.67 ( 595) hydrogen bonds : angle 3.99539 / 2.74 ( 1668) Misc. bond : bond 0.00010 / 0.00 ( 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 147 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 23 GLN cc_start: 0.7651 (mt0) cc_final: 0.7347 (tt0) REVERT: A 203 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 256 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: A 386 LYS cc_start: 0.8019 (tptt) cc_final: 0.7758 (mtmt) REVERT: B 7 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: B 103 GLU cc_start: 0.7686 (tt0) cc_final: 0.7456 (mt-10) REVERT: B 110 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7854 (mmpt) REVERT: B 141 ARG cc_start: 0.8326 (mmm160) cc_final: 0.8047 (mmt90) REVERT: B 311 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 497 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 500 LEU cc_start: 0.7768 (mt) cc_final: 0.7537 (pt) REVERT: C 430 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: C 511 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7209 (mm-30) REVERT: C 786 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7279 (mt-10) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 1.3778 time to fit residues: 211.8737 Evaluate side-chains 146 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 B residue 7 GLU Chi-restraints excluded: chain B residue 42 ASP 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 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 513 MET Chi-restraints excluded: chain C residue 593 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN C 392 HIS ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121845 restraints weight = 40833.902| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.15 r_work: 0.3442 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12845 Z= 0.098 Angle : 0.466 5.910 17384 Z= 0.246 Chirality : 0.038 0.142 1935 Planarity : 0.004 0.039 2219 Dihedral : 5.414 57.209 1732 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.25 % Favored : 97.62 % Rotamer: Outliers : 1.73 % Allowed : 20.59 % Favored : 77.68 % 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: 1.16 (0.22), residues: 1555 helix: 1.68 (0.19), residues: 800 sheet: 0.20 (0.40), residues: 145 loop : -0.23 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 773 TYR 0.011 0.001 TYR A 320 PHE 0.010 0.001 PHE A 166 TRP 0.011 0.001 TRP B 26 HIS 0.002 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (12844) covalent geometry : angle 0.46644 / 0.25 (17384) hydrogen bonds : bond 0.04755 / 3.13 ( 595) hydrogen bonds : angle 3.91254 / 2.68 ( 1668) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9600.48 seconds wall clock time: 162 minutes 21.65 seconds (9741.65 seconds total)