Starting phenix.real_space_refine on Sun Aug 24 20:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.map" model { file = "/net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9la0_62915/08_2025/9la0_62915.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 14236 2.51 5 N 3656 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21944 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "B" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "C" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "D" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Time building chain proxies: 4.29, per 1000 atoms: 0.20 Number of scatterers: 21944 At special positions: 0 Unit cell: (125.292, 125.292, 180.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3952 8.00 N 3656 7.00 C 14236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 953.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 11 sheets defined 69.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.544A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 97 through 115 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.513A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.036A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.620A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 removed outlier: 4.269A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.635A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.767A pdb=" N LYS A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 576 through 587 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 706 through 724 Processing helix chain 'B' and resid 62 through 89 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.945A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.526A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 177 through 191 removed outlier: 4.300A pdb=" N VAL B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.020A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.818A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.626A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.880A pdb=" N ASP B 363 " --> pdb=" O MET B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.532A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.650A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 511 removed outlier: 3.752A pdb=" N GLU B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.541A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 587 Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 628 through 639 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.589A pdb=" N GLY B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 685 removed outlier: 4.273A pdb=" N ALA B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 706 through 724 removed outlier: 3.725A pdb=" N ILE B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 96 through 116 removed outlier: 4.529A pdb=" N LEU C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.538A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 3.962A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.548A pdb=" N TYR C 233 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.567A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 353 Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.709A pdb=" N ASP C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 377 Processing helix chain 'C' and resid 377 through 384 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.940A pdb=" N GLU C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.633A pdb=" N SER C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.819A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 586 Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 619 Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 651 Processing helix chain 'C' and resid 663 through 672 removed outlier: 3.662A pdb=" N VAL C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 706 through 722 removed outlier: 4.003A pdb=" N ALA C 719 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 722 " --> pdb=" O ASN C 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 removed outlier: 3.708A pdb=" N VAL D 74 " --> pdb=" O MET D 70 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.604A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.409A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 removed outlier: 3.883A pdb=" N ARG D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.501A pdb=" N ASP D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.567A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 195 through 226 removed outlier: 4.278A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.918A pdb=" N TYR D 233 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.600A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 Processing helix chain 'D' and resid 336 through 354 Processing helix chain 'D' and resid 357 through 364 removed outlier: 3.741A pdb=" N ASP D 363 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 4.286A pdb=" N LEU D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) Proline residue: D 379 - end of helix removed outlier: 3.851A pdb=" N LYS D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 401 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 492 through 506 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 529 through 542 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 609 through 619 removed outlier: 3.553A pdb=" N GLU D 619 " --> pdb=" O LEU D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.602A pdb=" N LEU D 644 " --> pdb=" O ASP D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 724 removed outlier: 4.055A pdb=" N SER D 722 " --> pdb=" O ASN D 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.661A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.453A pdb=" N HIS A 476 " --> pdb=" O CYS A 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.633A pdb=" N VAL A 469 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.654A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.535A pdb=" N HIS B 476 " --> pdb=" O CYS B 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.766A pdb=" N VAL B 469 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.412A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 412 through 414 removed outlier: 3.766A pdb=" N THR C 414 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 434 through 436 removed outlier: 3.501A pdb=" N GLU C 443 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.709A pdb=" N HIS D 476 " --> pdb=" O CYS D 427 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 452 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 412 through 414 removed outlier: 6.647A pdb=" N VAL D 469 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 433 " --> pdb=" O VAL D 445 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3885 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: 3.03 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6961 1.34 - 1.46: 4405 1.46 - 1.58: 10938 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 22460 Sorted by residual: bond pdb=" N ASP D 561 " pdb=" CA ASP D 561 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N ILE A 194 " pdb=" CA ILE A 194 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.35e+00 bond pdb=" N ILE B 277 " pdb=" CA ILE B 277 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.17e+00 bond pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.06e+00 bond pdb=" N ILE B 266 " pdb=" CA ILE B 266 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.06e+00 ... (remaining 22455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 29012 1.97 - 3.94: 1205 3.94 - 5.91: 122 5.91 - 7.88: 35 7.88 - 9.84: 10 Bond angle restraints: 30384 Sorted by residual: angle pdb=" N ASP A 495 " pdb=" CA ASP A 495 " pdb=" C ASP A 495 " ideal model delta sigma weight residual 111.75 105.55 6.20 1.28e+00 6.10e-01 2.35e+01 angle pdb=" N TYR D 355 " pdb=" CA TYR D 355 " pdb=" C TYR D 355 " ideal model delta sigma weight residual 112.38 106.76 5.62 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N PRO B 654 " pdb=" CA PRO B 654 " pdb=" C PRO B 654 " ideal model delta sigma weight residual 114.35 108.80 5.55 1.25e+00 6.40e-01 1.97e+01 angle pdb=" N GLY D 455 " pdb=" CA GLY D 455 " pdb=" C GLY D 455 " ideal model delta sigma weight residual 115.08 108.34 6.74 1.54e+00 4.22e-01 1.92e+01 angle pdb=" N PRO B 664 " pdb=" CA PRO B 664 " pdb=" C PRO B 664 " ideal model delta sigma weight residual 113.75 107.36 6.39 1.49e+00 4.50e-01 1.84e+01 ... (remaining 30379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 11293 16.07 - 32.13: 1426 32.13 - 48.20: 405 48.20 - 64.26: 158 64.26 - 80.33: 22 Dihedral angle restraints: 13304 sinusoidal: 5396 harmonic: 7908 Sorted by residual: dihedral pdb=" CA ILE B 551 " pdb=" C ILE B 551 " pdb=" N ARG B 552 " pdb=" CA ARG B 552 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA CYS A 461 " pdb=" C CYS A 461 " pdb=" N ASN A 462 " pdb=" CA ASN A 462 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS D 523 " pdb=" C HIS D 523 " pdb=" N ILE D 524 " pdb=" CA ILE D 524 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 13301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2823 0.069 - 0.138: 466 0.138 - 0.207: 72 0.207 - 0.276: 14 0.276 - 0.345: 1 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CG LEU B 516 " pdb=" CB LEU B 516 " pdb=" CD1 LEU B 516 " pdb=" CD2 LEU B 516 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ILE D 277 " pdb=" N ILE D 277 " pdb=" C ILE D 277 " pdb=" CB ILE D 277 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ILE B 723 " pdb=" N ILE B 723 " pdb=" C ILE B 723 " pdb=" CB ILE B 723 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3373 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 318 " -0.276 9.50e-02 1.11e+02 1.24e-01 9.57e+00 pdb=" NE ARG D 318 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 318 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 318 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 318 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 329 " 0.020 2.00e-02 2.50e+03 1.97e-02 6.76e+00 pdb=" CG PHE D 329 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 329 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 329 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE D 329 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE D 329 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 329 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.221 9.50e-02 1.11e+02 9.92e-02 6.04e+00 pdb=" NE ARG A 497 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " 0.008 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 531 2.69 - 3.24: 23616 3.24 - 3.79: 37945 3.79 - 4.35: 51449 4.35 - 4.90: 79558 Nonbonded interactions: 193099 Sorted by model distance: nonbonded pdb=" OD1 ASP D 658 " pdb=" N TYR D 659 " model vdw 2.132 3.120 nonbonded pdb=" OG SER A 622 " pdb=" OD1 ASN A 624 " model vdw 2.203 3.040 nonbonded pdb=" O ILE B 194 " pdb=" NH2 ARG C 320 " model vdw 2.207 3.120 nonbonded pdb=" O LYS D 526 " pdb=" N GLU D 530 " model vdw 2.207 3.120 nonbonded pdb=" O PRO D 379 " pdb=" NZ LYS D 383 " model vdw 2.208 3.120 ... (remaining 193094 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22460 Z= 0.356 Angle : 0.850 9.844 30384 Z= 0.541 Chirality : 0.054 0.345 3376 Planarity : 0.006 0.124 3832 Dihedral : 16.515 80.325 8232 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.43 % Allowed : 22.32 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 2696 helix: 0.44 (0.12), residues: 1701 sheet: -2.48 (0.52), residues: 69 loop : -0.36 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 497 TYR 0.039 0.002 TYR C 196 PHE 0.044 0.002 PHE D 329 TRP 0.026 0.002 TRP B 68 HIS 0.027 0.002 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00550 (22460) covalent geometry : angle 0.85005 (30384) hydrogen bonds : bond 0.13999 ( 1341) hydrogen bonds : angle 6.55318 ( 3885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 540 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7841 (mmm160) cc_final: 0.6795 (mtm110) REVERT: A 64 TRP cc_start: 0.8048 (m100) cc_final: 0.6106 (t60) REVERT: A 70 MET cc_start: 0.7983 (tpt) cc_final: 0.7698 (tmm) REVERT: A 96 ARG cc_start: 0.8397 (ptm160) cc_final: 0.6715 (tmt170) REVERT: A 101 ASP cc_start: 0.7278 (t70) cc_final: 0.7051 (t0) REVERT: A 124 GLN cc_start: 0.8458 (mt0) cc_final: 0.8008 (mp10) REVERT: A 140 LEU cc_start: 0.8835 (mp) cc_final: 0.8626 (mp) REVERT: A 146 MET cc_start: 0.7329 (mmt) cc_final: 0.6775 (mmp) REVERT: A 320 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7261 (tpt-90) REVERT: A 363 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7872 (p0) REVERT: A 403 HIS cc_start: 0.7327 (m-70) cc_final: 0.7097 (m-70) REVERT: A 404 GLU cc_start: 0.7819 (pt0) cc_final: 0.7333 (pt0) REVERT: A 405 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6823 (mm-30) REVERT: A 415 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8269 (tm-30) REVERT: A 430 LEU cc_start: 0.8441 (tp) cc_final: 0.8237 (tt) REVERT: A 676 MET cc_start: 0.8431 (mmt) cc_final: 0.7837 (mmt) REVERT: A 679 MET cc_start: 0.8472 (mtm) cc_final: 0.8192 (ptm) REVERT: B 56 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5141 (m-10) REVERT: B 70 MET cc_start: 0.7610 (tpp) cc_final: 0.7360 (mmt) REVERT: B 295 ASP cc_start: 0.8337 (t0) cc_final: 0.8092 (t70) REVERT: B 296 MET cc_start: 0.8526 (ttp) cc_final: 0.8286 (ttt) REVERT: B 388 LYS cc_start: 0.7719 (tppt) cc_final: 0.6853 (pttp) REVERT: B 421 ASP cc_start: 0.8487 (m-30) cc_final: 0.7893 (t70) REVERT: B 428 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7570 (pm20) REVERT: B 470 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7772 (ttp80) REVERT: B 479 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8169 (ttp80) REVERT: B 482 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8396 (ttmt) REVERT: B 602 PHE cc_start: 0.7590 (t80) cc_final: 0.7274 (t80) REVERT: B 623 PHE cc_start: 0.5564 (p90) cc_final: 0.4407 (p90) REVERT: B 652 MET cc_start: 0.6916 (mtt) cc_final: 0.6582 (mmm) REVERT: B 659 TYR cc_start: 0.6303 (p90) cc_final: 0.4284 (p90) REVERT: B 666 HIS cc_start: 0.5051 (OUTLIER) cc_final: 0.4715 (t-170) REVERT: C 121 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6157 (tmt170) REVERT: C 193 ARG cc_start: 0.6659 (tmt170) cc_final: 0.6200 (ttp-110) REVERT: C 317 GLU cc_start: 0.8038 (tt0) cc_final: 0.7373 (tm-30) REVERT: C 337 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6798 (mtp85) REVERT: C 346 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7557 (m170) REVERT: C 362 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8076 (mt0) REVERT: C 371 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8014 (mttt) REVERT: C 381 ILE cc_start: 0.8711 (mm) cc_final: 0.8509 (mm) REVERT: C 421 ASP cc_start: 0.7692 (m-30) cc_final: 0.6500 (t70) REVERT: C 422 HIS cc_start: 0.8049 (m-70) cc_final: 0.7605 (m-70) REVERT: C 430 LEU cc_start: 0.8232 (tp) cc_final: 0.8019 (tp) REVERT: C 454 PHE cc_start: 0.8588 (p90) cc_final: 0.8374 (p90) REVERT: C 493 PHE cc_start: 0.6584 (p90) cc_final: 0.6155 (p90) REVERT: C 494 HIS cc_start: 0.7858 (m-70) cc_final: 0.7384 (m-70) REVERT: C 500 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7697 (mt) REVERT: C 536 ASN cc_start: 0.7968 (m-40) cc_final: 0.7681 (t0) REVERT: C 543 ASP cc_start: 0.7791 (t0) cc_final: 0.7512 (t0) REVERT: C 623 PHE cc_start: 0.6686 (m-80) cc_final: 0.6102 (m-80) REVERT: C 626 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7029 (mp0) REVERT: C 631 PHE cc_start: 0.8966 (t80) cc_final: 0.8761 (t80) REVERT: C 633 CYS cc_start: 0.9209 (m) cc_final: 0.8661 (p) REVERT: C 641 SER cc_start: 0.9033 (p) cc_final: 0.8555 (m) REVERT: C 655 ASN cc_start: 0.8504 (m-40) cc_final: 0.8170 (m110) REVERT: C 659 TYR cc_start: 0.6974 (p90) cc_final: 0.6751 (p90) REVERT: D 64 TRP cc_start: 0.6032 (t-100) cc_final: 0.5777 (t-100) REVERT: D 134 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7067 (tpt-90) REVERT: D 281 ASN cc_start: 0.8169 (m-40) cc_final: 0.7870 (m-40) REVERT: D 289 MET cc_start: 0.8830 (mtp) cc_final: 0.8621 (mtp) REVERT: D 291 TYR cc_start: 0.9036 (t80) cc_final: 0.8601 (t80) REVERT: D 318 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7333 (ptp-110) REVERT: D 352 ASP cc_start: 0.6898 (t0) cc_final: 0.6135 (m-30) REVERT: D 355 TYR cc_start: 0.5846 (OUTLIER) cc_final: 0.5050 (t80) REVERT: D 364 ILE cc_start: 0.8616 (mt) cc_final: 0.8340 (tp) REVERT: D 404 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 676 MET cc_start: 0.9339 (mtp) cc_final: 0.9094 (mtm) REVERT: D 700 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8097 (tp30) outliers start: 82 outliers final: 30 residues processed: 592 average time/residue: 0.1481 time to fit residues: 132.4767 Evaluate side-chains 406 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 368 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 403 HIS A 451 HIS A 462 ASN A 502 ASN A 510 ASN A 661 HIS A 706 ASN B 186 GLN B 331 ASN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 494 HIS B 541 GLN B 558 ASN B 624 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS B 695 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN C 354 HIS C 403 HIS C 523 HIS ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN D 354 HIS D 403 HIS D 695 ASN D 718 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115968 restraints weight = 36243.248| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.90 r_work: 0.3453 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22460 Z= 0.174 Angle : 0.675 10.053 30384 Z= 0.349 Chirality : 0.044 0.340 3376 Planarity : 0.004 0.061 3832 Dihedral : 6.773 73.517 3058 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.57 % Allowed : 20.90 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.16), residues: 2696 helix: 0.99 (0.12), residues: 1720 sheet: -1.79 (0.46), residues: 90 loop : -0.23 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 497 TYR 0.025 0.002 TYR D 130 PHE 0.026 0.002 PHE A 407 TRP 0.026 0.002 TRP B 693 HIS 0.017 0.002 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00386 (22460) covalent geometry : angle 0.67529 (30384) hydrogen bonds : bond 0.05525 ( 1341) hydrogen bonds : angle 5.32923 ( 3885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 413 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.6140 (m-80) cc_final: 0.5847 (m-80) REVERT: A 63 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7033 (mtm110) REVERT: A 64 TRP cc_start: 0.7989 (m100) cc_final: 0.6449 (t60) REVERT: A 96 ARG cc_start: 0.8161 (ptm160) cc_final: 0.6935 (tmt-80) REVERT: A 124 GLN cc_start: 0.8512 (mt0) cc_final: 0.8219 (mp10) REVERT: A 405 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 562 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: A 676 MET cc_start: 0.8346 (mmt) cc_final: 0.7818 (mmt) REVERT: B 56 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5068 (m-10) REVERT: B 64 TRP cc_start: 0.6865 (m100) cc_final: 0.6436 (m-10) REVERT: B 352 ASP cc_start: 0.7937 (t70) cc_final: 0.7609 (t0) REVERT: B 377 TYR cc_start: 0.8354 (m-10) cc_final: 0.8107 (m-80) REVERT: B 388 LYS cc_start: 0.8070 (tppt) cc_final: 0.7292 (pttp) REVERT: B 408 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7773 (mt) REVERT: B 420 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7354 (p) REVERT: B 421 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8023 (t0) REVERT: B 456 ASP cc_start: 0.8338 (p0) cc_final: 0.8050 (p0) REVERT: B 470 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7806 (ttp80) REVERT: B 479 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8254 (ttp80) REVERT: B 480 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 482 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8466 (ttmt) REVERT: B 500 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 504 MET cc_start: 0.7709 (mmm) cc_final: 0.7384 (mpp) REVERT: B 534 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8152 (mttt) REVERT: B 623 PHE cc_start: 0.5410 (p90) cc_final: 0.4280 (p90) REVERT: C 121 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6423 (tmt170) REVERT: C 317 GLU cc_start: 0.7885 (tt0) cc_final: 0.7581 (tm-30) REVERT: C 332 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7767 (ttm170) REVERT: C 337 ARG cc_start: 0.7197 (mtp85) cc_final: 0.6928 (mtp85) REVERT: C 371 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8330 (mttt) REVERT: C 421 ASP cc_start: 0.7645 (m-30) cc_final: 0.6682 (t70) REVERT: C 422 HIS cc_start: 0.8092 (m-70) cc_final: 0.7752 (m-70) REVERT: C 493 PHE cc_start: 0.6402 (p90) cc_final: 0.6085 (p90) REVERT: C 494 HIS cc_start: 0.7783 (m-70) cc_final: 0.7416 (m-70) REVERT: C 502 ASN cc_start: 0.7653 (t0) cc_final: 0.7046 (t0) REVERT: C 536 ASN cc_start: 0.7915 (m-40) cc_final: 0.7707 (t0) REVERT: C 623 PHE cc_start: 0.6426 (m-80) cc_final: 0.6145 (m-80) REVERT: C 626 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7294 (mp0) REVERT: C 635 THR cc_start: 0.8851 (m) cc_final: 0.8644 (p) REVERT: C 652 MET cc_start: 0.6078 (tpt) cc_final: 0.5878 (tpt) REVERT: C 706 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8024 (t0) REVERT: D 64 TRP cc_start: 0.6241 (t-100) cc_final: 0.6028 (t-100) REVERT: D 134 ARG cc_start: 0.7462 (mmm160) cc_final: 0.6960 (mmm160) REVERT: D 289 MET cc_start: 0.8748 (mtp) cc_final: 0.8545 (mtp) REVERT: D 355 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.4354 (t80) REVERT: D 404 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8000 (mt-10) REVERT: D 493 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.5921 (t80) REVERT: D 504 MET cc_start: 0.7889 (mtp) cc_final: 0.7686 (mtp) REVERT: D 673 LEU cc_start: 0.8381 (tp) cc_final: 0.8099 (tt) REVERT: D 676 MET cc_start: 0.9242 (mtp) cc_final: 0.8715 (mtt) REVERT: D 679 MET cc_start: 0.8482 (mtt) cc_final: 0.8061 (mtp) REVERT: D 700 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7951 (tp30) REVERT: D 709 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7769 (mm) outliers start: 133 outliers final: 73 residues processed: 509 average time/residue: 0.1402 time to fit residues: 111.0881 Evaluate side-chains 421 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 337 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 493 PHE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 224 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 201 optimal weight: 10.9990 chunk 166 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 510 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN C 59 HIS C 523 HIS C 718 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 510 ASN ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.169989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112871 restraints weight = 36230.023| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.57 r_work: 0.3335 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22460 Z= 0.194 Angle : 0.645 11.928 30384 Z= 0.330 Chirality : 0.043 0.249 3376 Planarity : 0.004 0.046 3832 Dihedral : 6.307 69.835 3040 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.99 % Allowed : 20.52 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2696 helix: 0.98 (0.12), residues: 1731 sheet: -1.51 (0.47), residues: 93 loop : -0.21 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 702 TYR 0.018 0.002 TYR A 562 PHE 0.022 0.002 PHE A 582 TRP 0.026 0.001 TRP B 693 HIS 0.011 0.001 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00444 (22460) covalent geometry : angle 0.64459 (30384) hydrogen bonds : bond 0.05052 ( 1341) hydrogen bonds : angle 5.09509 ( 3885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 384 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7009 (mtm110) REVERT: A 64 TRP cc_start: 0.8112 (m100) cc_final: 0.6421 (t60) REVERT: A 96 ARG cc_start: 0.8220 (ptm160) cc_final: 0.6809 (tmt-80) REVERT: A 124 GLN cc_start: 0.8632 (mt0) cc_final: 0.7978 (tt0) REVERT: A 324 ASN cc_start: 0.8132 (m-40) cc_final: 0.7882 (m110) REVERT: A 401 ARG cc_start: 0.8375 (mmt90) cc_final: 0.8074 (mmt-90) REVERT: A 526 LYS cc_start: 0.8484 (mttt) cc_final: 0.8219 (mtpt) REVERT: A 676 MET cc_start: 0.8536 (mmt) cc_final: 0.8107 (mmm) REVERT: B 56 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.5162 (m-10) REVERT: B 64 TRP cc_start: 0.7013 (m100) cc_final: 0.6528 (m-10) REVERT: B 295 ASP cc_start: 0.8477 (t70) cc_final: 0.8186 (t0) REVERT: B 334 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7401 (mmtt) REVERT: B 352 ASP cc_start: 0.8089 (t70) cc_final: 0.7314 (t0) REVERT: B 377 TYR cc_start: 0.8491 (m-10) cc_final: 0.8196 (m-10) REVERT: B 388 LYS cc_start: 0.8096 (tppt) cc_final: 0.7222 (pttp) REVERT: B 421 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 456 ASP cc_start: 0.8362 (p0) cc_final: 0.7852 (p0) REVERT: B 470 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7764 (ttp80) REVERT: B 479 ARG cc_start: 0.8520 (tmm-80) cc_final: 0.8171 (ttp80) REVERT: B 480 LEU cc_start: 0.8815 (tt) cc_final: 0.8611 (tt) REVERT: B 482 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8471 (ttmt) REVERT: B 493 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7517 (p90) REVERT: B 534 LYS cc_start: 0.8426 (mmtp) cc_final: 0.8219 (mtmt) REVERT: B 623 PHE cc_start: 0.5300 (p90) cc_final: 0.4974 (p90) REVERT: B 644 LEU cc_start: 0.9039 (tp) cc_final: 0.8779 (mt) REVERT: C 121 ARG cc_start: 0.7370 (mtp85) cc_final: 0.6513 (tmt170) REVERT: C 129 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7802 (p) REVERT: C 317 GLU cc_start: 0.8149 (tt0) cc_final: 0.7659 (tm-30) REVERT: C 337 ARG cc_start: 0.7442 (mtp85) cc_final: 0.7142 (mtp85) REVERT: C 371 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8335 (mttt) REVERT: C 421 ASP cc_start: 0.7861 (m-30) cc_final: 0.6834 (t70) REVERT: C 493 PHE cc_start: 0.6450 (p90) cc_final: 0.6229 (p90) REVERT: C 500 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7808 (mt) REVERT: C 502 ASN cc_start: 0.7234 (t0) cc_final: 0.6958 (t0) REVERT: C 626 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7420 (mp0) REVERT: C 666 HIS cc_start: 0.7330 (m90) cc_final: 0.7119 (m90) REVERT: D 64 TRP cc_start: 0.6402 (t-100) cc_final: 0.6155 (t-100) REVERT: D 134 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7000 (mmm160) REVERT: D 326 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 354 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6219 (m170) REVERT: D 533 LEU cc_start: 0.8532 (mt) cc_final: 0.8085 (mp) REVERT: D 644 LEU cc_start: 0.9337 (pp) cc_final: 0.9105 (pp) REVERT: D 673 LEU cc_start: 0.8436 (tp) cc_final: 0.8099 (tt) REVERT: D 676 MET cc_start: 0.9324 (mtp) cc_final: 0.8609 (mtt) REVERT: D 679 MET cc_start: 0.8654 (mtt) cc_final: 0.8399 (mtt) REVERT: D 700 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8023 (tp30) REVERT: D 709 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7675 (mt) outliers start: 143 outliers final: 85 residues processed: 484 average time/residue: 0.1307 time to fit residues: 99.2534 Evaluate side-chains 422 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 328 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 0.6980 chunk 259 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 160 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 HIS B 281 ASN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN C 706 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111274 restraints weight = 36080.110| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.56 r_work: 0.3327 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22460 Z= 0.176 Angle : 0.632 10.681 30384 Z= 0.324 Chirality : 0.043 0.208 3376 Planarity : 0.004 0.042 3832 Dihedral : 6.197 74.129 3031 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.82 % Allowed : 20.35 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2696 helix: 1.05 (0.12), residues: 1731 sheet: -1.30 (0.46), residues: 98 loop : -0.16 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 497 TYR 0.016 0.002 TYR C 562 PHE 0.027 0.002 PHE D 540 TRP 0.018 0.001 TRP B 693 HIS 0.009 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00405 (22460) covalent geometry : angle 0.63165 (30384) hydrogen bonds : bond 0.04802 ( 1341) hydrogen bonds : angle 4.95176 ( 3885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 358 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7782 (mmm160) cc_final: 0.6656 (mtm110) REVERT: A 96 ARG cc_start: 0.8030 (ptm160) cc_final: 0.6437 (tmt170) REVERT: A 124 GLN cc_start: 0.8386 (mt0) cc_final: 0.7709 (tt0) REVERT: A 146 MET cc_start: 0.7165 (mmt) cc_final: 0.6694 (mmt) REVERT: A 324 ASN cc_start: 0.7958 (m-40) cc_final: 0.7621 (m110) REVERT: A 325 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8631 (t0) REVERT: A 516 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.3290 (tp) REVERT: A 527 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: A 676 MET cc_start: 0.8722 (mmt) cc_final: 0.8131 (mmt) REVERT: A 679 MET cc_start: 0.8547 (mtp) cc_final: 0.7929 (ptm) REVERT: B 56 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: B 64 TRP cc_start: 0.6747 (m100) cc_final: 0.6220 (m-10) REVERT: B 139 TYR cc_start: 0.8546 (t80) cc_final: 0.8344 (t80) REVERT: B 295 ASP cc_start: 0.8399 (t70) cc_final: 0.8040 (t0) REVERT: B 334 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7150 (mmtt) REVERT: B 352 ASP cc_start: 0.7483 (t70) cc_final: 0.7269 (t0) REVERT: B 377 TYR cc_start: 0.8057 (m-10) cc_final: 0.7819 (m-10) REVERT: B 388 LYS cc_start: 0.8054 (tppt) cc_final: 0.7015 (pttp) REVERT: B 420 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.6977 (p) REVERT: B 421 ASP cc_start: 0.8460 (m-30) cc_final: 0.7987 (t0) REVERT: B 422 HIS cc_start: 0.8281 (m-70) cc_final: 0.7948 (m-70) REVERT: B 456 ASP cc_start: 0.8562 (p0) cc_final: 0.8014 (p0) REVERT: B 470 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7573 (ttp80) REVERT: B 479 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7833 (ttp80) REVERT: B 482 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8579 (tptp) REVERT: B 493 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7465 (p90) REVERT: C 121 ARG cc_start: 0.7242 (mtp85) cc_final: 0.6286 (tmt170) REVERT: C 317 GLU cc_start: 0.8301 (tt0) cc_final: 0.7524 (tm-30) REVERT: C 337 ARG cc_start: 0.7143 (mtp85) cc_final: 0.6839 (mtp85) REVERT: C 371 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7923 (mttt) REVERT: C 421 ASP cc_start: 0.7785 (m-30) cc_final: 0.6532 (t70) REVERT: C 493 PHE cc_start: 0.6388 (p90) cc_final: 0.6042 (p90) REVERT: C 626 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7323 (mp0) REVERT: C 655 ASN cc_start: 0.8690 (t0) cc_final: 0.8442 (p0) REVERT: C 666 HIS cc_start: 0.7297 (m90) cc_final: 0.7056 (m90) REVERT: D 64 TRP cc_start: 0.6001 (t-100) cc_final: 0.5676 (t-100) REVERT: D 134 ARG cc_start: 0.7492 (mmm160) cc_final: 0.7058 (mmm160) REVERT: D 301 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7621 (t80) REVERT: D 326 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7939 (mp) REVERT: D 354 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6603 (m170) REVERT: D 357 ASP cc_start: 0.6799 (p0) cc_final: 0.6562 (p0) REVERT: D 362 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: D 388 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7552 (tmtt) REVERT: D 442 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7209 (mt-10) REVERT: D 644 LEU cc_start: 0.9278 (pp) cc_final: 0.8986 (pp) REVERT: D 673 LEU cc_start: 0.8397 (tp) cc_final: 0.8149 (tt) REVERT: D 676 MET cc_start: 0.9444 (mtp) cc_final: 0.8862 (mtt) REVERT: D 679 MET cc_start: 0.8705 (mtt) cc_final: 0.8396 (mtp) REVERT: D 700 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8149 (tp30) REVERT: D 709 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7743 (mt) outliers start: 139 outliers final: 90 residues processed: 458 average time/residue: 0.1212 time to fit residues: 88.6049 Evaluate side-chains 425 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 323 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 221 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 265 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 502 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS D 354 HIS ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.170325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111356 restraints weight = 35798.784| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.15 r_work: 0.3364 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22460 Z= 0.145 Angle : 0.606 10.070 30384 Z= 0.309 Chirality : 0.042 0.171 3376 Planarity : 0.004 0.046 3832 Dihedral : 5.872 54.553 3026 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.23 % Allowed : 21.06 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.16), residues: 2696 helix: 1.08 (0.12), residues: 1740 sheet: -1.10 (0.46), residues: 99 loop : -0.14 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 497 TYR 0.023 0.001 TYR A 562 PHE 0.021 0.002 PHE C 623 TRP 0.041 0.002 TRP B 693 HIS 0.010 0.001 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00323 (22460) covalent geometry : angle 0.60593 (30384) hydrogen bonds : bond 0.04529 ( 1341) hydrogen bonds : angle 4.80262 ( 3885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 357 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7783 (mmm160) cc_final: 0.6634 (mtm110) REVERT: A 96 ARG cc_start: 0.8026 (ptm160) cc_final: 0.6467 (tmt170) REVERT: A 124 GLN cc_start: 0.8397 (mt0) cc_final: 0.7742 (tt0) REVERT: A 146 MET cc_start: 0.7132 (mmt) cc_final: 0.6689 (mmt) REVERT: A 325 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8641 (t0) REVERT: A 401 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7812 (mmt-90) REVERT: A 516 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.3254 (tp) REVERT: A 527 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: A 676 MET cc_start: 0.8737 (mmt) cc_final: 0.8298 (mmt) REVERT: B 56 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.5106 (m-10) REVERT: B 64 TRP cc_start: 0.6733 (m100) cc_final: 0.6202 (m-10) REVERT: B 139 TYR cc_start: 0.8560 (t80) cc_final: 0.8316 (t80) REVERT: B 194 ILE cc_start: 0.8118 (mm) cc_final: 0.7840 (mm) REVERT: B 295 ASP cc_start: 0.8277 (t70) cc_final: 0.7934 (t0) REVERT: B 334 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7265 (mmtt) REVERT: B 388 LYS cc_start: 0.8052 (tppt) cc_final: 0.7028 (pttp) REVERT: B 421 ASP cc_start: 0.8444 (m-30) cc_final: 0.7999 (t0) REVERT: B 422 HIS cc_start: 0.8290 (m-70) cc_final: 0.8006 (m-70) REVERT: B 456 ASP cc_start: 0.8473 (p0) cc_final: 0.7903 (p0) REVERT: B 470 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7700 (ttp-110) REVERT: B 479 ARG cc_start: 0.8224 (tmm-80) cc_final: 0.7757 (ttp80) REVERT: B 482 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8592 (tptp) REVERT: B 493 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7373 (p90) REVERT: B 517 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5764 (mp0) REVERT: C 78 TYR cc_start: 0.8620 (t80) cc_final: 0.8369 (t80) REVERT: C 121 ARG cc_start: 0.7381 (mtp85) cc_final: 0.6441 (tmt170) REVERT: C 205 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 317 GLU cc_start: 0.8293 (tt0) cc_final: 0.7511 (tm-30) REVERT: C 320 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8420 (mmm-85) REVERT: C 323 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6720 (tpp) REVERT: C 337 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6834 (mtp85) REVERT: C 348 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7779 (mtp85) REVERT: C 371 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7944 (mttt) REVERT: C 421 ASP cc_start: 0.7621 (m-30) cc_final: 0.6447 (t70) REVERT: C 427 CYS cc_start: 0.7253 (m) cc_final: 0.6777 (t) REVERT: C 493 PHE cc_start: 0.6320 (p90) cc_final: 0.5953 (p90) REVERT: C 626 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7365 (mp0) REVERT: C 655 ASN cc_start: 0.8655 (t0) cc_final: 0.8361 (p0) REVERT: C 666 HIS cc_start: 0.7324 (m90) cc_final: 0.7070 (m90) REVERT: C 676 MET cc_start: 0.7871 (mmp) cc_final: 0.7528 (mmt) REVERT: D 64 TRP cc_start: 0.6111 (t-100) cc_final: 0.5833 (t-100) REVERT: D 134 ARG cc_start: 0.7462 (mmm160) cc_final: 0.7026 (mmm160) REVERT: D 301 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7624 (t80) REVERT: D 323 MET cc_start: 0.8276 (tpp) cc_final: 0.8016 (tpp) REVERT: D 326 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7952 (mp) REVERT: D 354 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6546 (m170) REVERT: D 357 ASP cc_start: 0.6695 (p0) cc_final: 0.6450 (p0) REVERT: D 362 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: D 369 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8377 (ttm110) REVERT: D 388 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7553 (tmtt) REVERT: D 442 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7325 (mt-10) REVERT: D 644 LEU cc_start: 0.9314 (pp) cc_final: 0.9107 (pp) REVERT: D 676 MET cc_start: 0.9432 (mtp) cc_final: 0.8700 (mtt) REVERT: D 700 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8256 (tp30) REVERT: D 709 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7890 (mt) outliers start: 125 outliers final: 82 residues processed: 450 average time/residue: 0.1301 time to fit residues: 91.9448 Evaluate side-chains 424 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 328 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 523 HIS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 227 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 chunk 166 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 346 HIS ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.169996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111702 restraints weight = 35801.259| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22460 Z= 0.136 Angle : 0.594 10.433 30384 Z= 0.303 Chirality : 0.041 0.166 3376 Planarity : 0.004 0.040 3832 Dihedral : 5.741 58.993 3024 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.52 % Allowed : 21.73 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.16), residues: 2696 helix: 1.16 (0.12), residues: 1740 sheet: -0.82 (0.47), residues: 100 loop : -0.09 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 497 TYR 0.020 0.001 TYR A 562 PHE 0.041 0.002 PHE D 540 TRP 0.024 0.001 TRP B 693 HIS 0.009 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00304 (22460) covalent geometry : angle 0.59412 (30384) hydrogen bonds : bond 0.04406 ( 1341) hydrogen bonds : angle 4.68270 ( 3885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 353 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.6040 (m-80) cc_final: 0.5753 (m-80) REVERT: A 63 ARG cc_start: 0.7799 (mmm160) cc_final: 0.6662 (mtm110) REVERT: A 96 ARG cc_start: 0.8001 (ptm160) cc_final: 0.6450 (tmt170) REVERT: A 124 GLN cc_start: 0.8399 (mt0) cc_final: 0.7744 (tt0) REVERT: A 146 MET cc_start: 0.7052 (mmt) cc_final: 0.6662 (mmt) REVERT: A 516 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.3280 (tp) REVERT: A 526 LYS cc_start: 0.8368 (mttt) cc_final: 0.8162 (mtpt) REVERT: A 527 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6723 (mp10) REVERT: A 644 LEU cc_start: 0.9381 (tp) cc_final: 0.9160 (tp) REVERT: A 676 MET cc_start: 0.8715 (mmt) cc_final: 0.8170 (mmt) REVERT: A 679 MET cc_start: 0.8594 (mtp) cc_final: 0.8054 (ptm) REVERT: B 56 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5061 (m-10) REVERT: B 64 TRP cc_start: 0.6743 (m100) cc_final: 0.6216 (m-10) REVERT: B 139 TYR cc_start: 0.8573 (t80) cc_final: 0.8320 (t80) REVERT: B 295 ASP cc_start: 0.8285 (t70) cc_final: 0.7949 (t0) REVERT: B 334 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7210 (mmtt) REVERT: B 421 ASP cc_start: 0.8415 (m-30) cc_final: 0.7984 (t0) REVERT: B 422 HIS cc_start: 0.8227 (m-70) cc_final: 0.7963 (m-70) REVERT: B 428 GLU cc_start: 0.7673 (pm20) cc_final: 0.7352 (pm20) REVERT: B 434 LEU cc_start: 0.7795 (mp) cc_final: 0.6905 (pp) REVERT: B 456 ASP cc_start: 0.8525 (p0) cc_final: 0.7973 (p0) REVERT: B 470 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7578 (ttp80) REVERT: B 479 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7768 (ttp80) REVERT: B 482 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8485 (tptp) REVERT: B 492 TYR cc_start: 0.8502 (m-80) cc_final: 0.8136 (m-80) REVERT: B 493 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7339 (p90) REVERT: B 495 ASP cc_start: 0.7649 (m-30) cc_final: 0.7371 (m-30) REVERT: B 652 MET cc_start: 0.7103 (tpp) cc_final: 0.6450 (mpp) REVERT: C 78 TYR cc_start: 0.8605 (t80) cc_final: 0.8351 (t80) REVERT: C 121 ARG cc_start: 0.7374 (mtp85) cc_final: 0.6432 (tmt170) REVERT: C 317 GLU cc_start: 0.8287 (tt0) cc_final: 0.7519 (tm-30) REVERT: C 323 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6755 (tpp) REVERT: C 337 ARG cc_start: 0.7149 (mtp85) cc_final: 0.6844 (mtp85) REVERT: C 348 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7749 (mtp85) REVERT: C 371 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7937 (mttt) REVERT: C 421 ASP cc_start: 0.7458 (m-30) cc_final: 0.6333 (t70) REVERT: C 493 PHE cc_start: 0.6332 (p90) cc_final: 0.5769 (p90) REVERT: C 494 HIS cc_start: 0.7954 (m-70) cc_final: 0.7653 (m-70) REVERT: C 601 LEU cc_start: 0.8872 (tp) cc_final: 0.8423 (pt) REVERT: C 626 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7484 (mp0) REVERT: C 655 ASN cc_start: 0.8656 (t0) cc_final: 0.8339 (p0) REVERT: D 64 TRP cc_start: 0.6093 (t-100) cc_final: 0.5803 (t-100) REVERT: D 127 ARG cc_start: 0.7495 (mmm160) cc_final: 0.6943 (mmm-85) REVERT: D 134 ARG cc_start: 0.7437 (mmm160) cc_final: 0.6832 (mmm160) REVERT: D 254 LEU cc_start: 0.8545 (tp) cc_final: 0.8276 (tp) REVERT: D 301 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7615 (t80) REVERT: D 323 MET cc_start: 0.8299 (tpp) cc_final: 0.8008 (tpp) REVERT: D 326 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7963 (mp) REVERT: D 354 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6848 (m170) REVERT: D 357 ASP cc_start: 0.6570 (p0) cc_final: 0.6320 (p0) REVERT: D 369 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8379 (ttm110) REVERT: D 388 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7631 (tmtt) REVERT: D 442 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7345 (mt-10) REVERT: D 515 LYS cc_start: 0.4601 (OUTLIER) cc_final: 0.3779 (mppt) REVERT: D 673 LEU cc_start: 0.8291 (tp) cc_final: 0.8018 (tt) REVERT: D 676 MET cc_start: 0.9326 (mtp) cc_final: 0.8858 (mtt) REVERT: D 700 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8267 (tp30) REVERT: D 709 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7889 (mt) outliers start: 108 outliers final: 79 residues processed: 434 average time/residue: 0.1379 time to fit residues: 93.1399 Evaluate side-chains 423 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 333 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 523 HIS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 134 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 374 GLN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 502 ASN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110875 restraints weight = 35924.827| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.50 r_work: 0.3335 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22460 Z= 0.169 Angle : 0.621 13.022 30384 Z= 0.314 Chirality : 0.043 0.422 3376 Planarity : 0.004 0.041 3832 Dihedral : 5.623 54.394 3022 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.11 % Allowed : 21.23 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2696 helix: 1.12 (0.12), residues: 1742 sheet: -1.00 (0.46), residues: 99 loop : -0.05 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 497 TYR 0.018 0.001 TYR A 562 PHE 0.043 0.002 PHE D 540 TRP 0.016 0.001 TRP B 693 HIS 0.009 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00390 (22460) covalent geometry : angle 0.62149 (30384) hydrogen bonds : bond 0.04423 ( 1341) hydrogen bonds : angle 4.71210 ( 3885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 347 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7836 (mmm160) cc_final: 0.6782 (mtm110) REVERT: A 96 ARG cc_start: 0.8017 (ptm160) cc_final: 0.6480 (tmt170) REVERT: A 124 GLN cc_start: 0.8350 (mt0) cc_final: 0.7675 (tt0) REVERT: A 146 MET cc_start: 0.7123 (mmt) cc_final: 0.6734 (mmt) REVERT: A 377 TYR cc_start: 0.7533 (m-10) cc_final: 0.7282 (m-80) REVERT: A 401 ARG cc_start: 0.8267 (mmt90) cc_final: 0.8012 (mmt90) REVERT: A 404 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 516 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.3285 (tp) REVERT: A 527 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: A 644 LEU cc_start: 0.9363 (tp) cc_final: 0.9126 (tp) REVERT: A 676 MET cc_start: 0.8713 (mmt) cc_final: 0.8186 (mmt) REVERT: A 679 MET cc_start: 0.8624 (mtp) cc_final: 0.8045 (ptm) REVERT: B 56 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.5038 (m-10) REVERT: B 64 TRP cc_start: 0.6794 (m100) cc_final: 0.6262 (m-10) REVERT: B 139 TYR cc_start: 0.8592 (t80) cc_final: 0.8312 (t80) REVERT: B 295 ASP cc_start: 0.8382 (t70) cc_final: 0.8068 (t0) REVERT: B 334 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7210 (mmtt) REVERT: B 421 ASP cc_start: 0.8450 (m-30) cc_final: 0.7951 (t0) REVERT: B 422 HIS cc_start: 0.8210 (m-70) cc_final: 0.7961 (m-70) REVERT: B 434 LEU cc_start: 0.7745 (mp) cc_final: 0.6968 (pp) REVERT: B 456 ASP cc_start: 0.8605 (p0) cc_final: 0.8051 (p0) REVERT: B 470 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7591 (ttp80) REVERT: B 482 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8466 (tptp) REVERT: B 492 TYR cc_start: 0.8504 (m-80) cc_final: 0.8226 (m-80) REVERT: B 495 ASP cc_start: 0.7683 (m-30) cc_final: 0.7463 (m-30) REVERT: B 652 MET cc_start: 0.7039 (tpp) cc_final: 0.6443 (mpp) REVERT: C 78 TYR cc_start: 0.8660 (t80) cc_final: 0.8395 (t80) REVERT: C 121 ARG cc_start: 0.7382 (mtp85) cc_final: 0.6421 (tmt170) REVERT: C 205 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (mt) REVERT: C 317 GLU cc_start: 0.8317 (tt0) cc_final: 0.7545 (tm-30) REVERT: C 337 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6826 (mtp85) REVERT: C 371 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7934 (mttt) REVERT: C 493 PHE cc_start: 0.6334 (p90) cc_final: 0.5729 (p90) REVERT: C 494 HIS cc_start: 0.7977 (m-70) cc_final: 0.7719 (m-70) REVERT: C 562 TYR cc_start: 0.7366 (p90) cc_final: 0.7122 (p90) REVERT: C 601 LEU cc_start: 0.8888 (tp) cc_final: 0.8468 (pt) REVERT: C 626 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7484 (mp0) REVERT: C 655 ASN cc_start: 0.8690 (t0) cc_final: 0.8302 (p0) REVERT: C 666 HIS cc_start: 0.7437 (m90) cc_final: 0.7173 (m-70) REVERT: D 64 TRP cc_start: 0.6123 (t-100) cc_final: 0.5820 (t-100) REVERT: D 127 ARG cc_start: 0.7541 (mmm160) cc_final: 0.7000 (mmm-85) REVERT: D 301 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7708 (t80) REVERT: D 323 MET cc_start: 0.8360 (tpp) cc_final: 0.8069 (tpp) REVERT: D 326 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7988 (mp) REVERT: D 369 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8469 (ttm110) REVERT: D 388 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7653 (tmtt) REVERT: D 442 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 515 LYS cc_start: 0.4619 (OUTLIER) cc_final: 0.3784 (mppt) REVERT: D 623 PHE cc_start: 0.5845 (m-80) cc_final: 0.5555 (m-10) REVERT: D 673 LEU cc_start: 0.8355 (tp) cc_final: 0.8024 (tt) REVERT: D 676 MET cc_start: 0.9303 (mtp) cc_final: 0.8927 (mtt) REVERT: D 700 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8301 (tp30) REVERT: D 709 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7906 (mt) outliers start: 122 outliers final: 91 residues processed: 437 average time/residue: 0.1292 time to fit residues: 89.9263 Evaluate side-chains 434 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 334 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN B 346 HIS B 403 HIS B 462 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 342 GLN C 502 ASN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.167487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108470 restraints weight = 35902.475| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.40 r_work: 0.3286 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22460 Z= 0.234 Angle : 0.672 14.587 30384 Z= 0.339 Chirality : 0.045 0.335 3376 Planarity : 0.004 0.038 3832 Dihedral : 5.690 59.237 3022 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.65 % Allowed : 21.98 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2696 helix: 1.04 (0.12), residues: 1732 sheet: -1.27 (0.45), residues: 99 loop : -0.02 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 497 TYR 0.020 0.002 TYR C 233 PHE 0.028 0.002 PHE D 540 TRP 0.013 0.002 TRP B 693 HIS 0.008 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00553 (22460) covalent geometry : angle 0.67165 (30384) hydrogen bonds : bond 0.04556 ( 1341) hydrogen bonds : angle 4.82232 ( 3885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 339 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7894 (mmm160) cc_final: 0.6855 (mtm110) REVERT: A 96 ARG cc_start: 0.8037 (ptm160) cc_final: 0.6621 (tmt170) REVERT: A 124 GLN cc_start: 0.8313 (mt0) cc_final: 0.7632 (tt0) REVERT: A 146 MET cc_start: 0.7216 (mmt) cc_final: 0.6810 (mmt) REVERT: A 324 ASN cc_start: 0.7977 (m-40) cc_final: 0.7629 (m110) REVERT: A 516 LEU cc_start: 0.4706 (OUTLIER) cc_final: 0.3234 (tp) REVERT: A 527 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: A 676 MET cc_start: 0.8726 (mmt) cc_final: 0.8227 (mmt) REVERT: B 64 TRP cc_start: 0.6787 (m100) cc_final: 0.6254 (m-10) REVERT: B 139 TYR cc_start: 0.8584 (t80) cc_final: 0.8268 (t80) REVERT: B 295 ASP cc_start: 0.8419 (t70) cc_final: 0.8072 (t0) REVERT: B 334 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7261 (mmtt) REVERT: B 421 ASP cc_start: 0.8458 (m-30) cc_final: 0.7936 (t0) REVERT: B 422 HIS cc_start: 0.8286 (m-70) cc_final: 0.7942 (m-70) REVERT: B 434 LEU cc_start: 0.7656 (mp) cc_final: 0.6929 (pp) REVERT: B 456 ASP cc_start: 0.8626 (p0) cc_final: 0.8105 (p0) REVERT: B 470 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7604 (ttp80) REVERT: B 482 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8470 (tptp) REVERT: B 652 MET cc_start: 0.7090 (tpp) cc_final: 0.6534 (mpp) REVERT: B 679 MET cc_start: 0.8209 (ptt) cc_final: 0.7956 (ptm) REVERT: C 121 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6520 (tmt170) REVERT: C 205 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8460 (mt) REVERT: C 317 GLU cc_start: 0.8351 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 337 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6820 (mtp85) REVERT: C 362 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8312 (mm-40) REVERT: C 371 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7912 (mttt) REVERT: C 493 PHE cc_start: 0.6309 (p90) cc_final: 0.5718 (p90) REVERT: C 494 HIS cc_start: 0.8075 (m-70) cc_final: 0.7834 (m-70) REVERT: C 562 TYR cc_start: 0.7359 (p90) cc_final: 0.7131 (p90) REVERT: C 601 LEU cc_start: 0.8888 (tp) cc_final: 0.8533 (pt) REVERT: C 626 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7483 (mp0) REVERT: C 655 ASN cc_start: 0.8726 (t0) cc_final: 0.8323 (p0) REVERT: C 666 HIS cc_start: 0.7565 (m90) cc_final: 0.7104 (m-70) REVERT: D 64 TRP cc_start: 0.6209 (t-100) cc_final: 0.5898 (t-100) REVERT: D 130 TYR cc_start: 0.7264 (m-80) cc_final: 0.6468 (m-80) REVERT: D 134 ARG cc_start: 0.7414 (mmm160) cc_final: 0.6833 (mmm160) REVERT: D 301 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7632 (t80) REVERT: D 326 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7921 (mp) REVERT: D 354 HIS cc_start: 0.6833 (t-90) cc_final: 0.6193 (m170) REVERT: D 388 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7681 (tmtt) REVERT: D 442 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7241 (mt-10) REVERT: D 515 LYS cc_start: 0.4728 (OUTLIER) cc_final: 0.3890 (mppt) REVERT: D 676 MET cc_start: 0.9287 (mtp) cc_final: 0.8918 (mtt) REVERT: D 700 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8417 (tp30) REVERT: D 709 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7959 (mt) outliers start: 111 outliers final: 89 residues processed: 423 average time/residue: 0.1336 time to fit residues: 89.4962 Evaluate side-chains 422 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 325 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** 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 = 0.4219 r_free = 0.4219 target = 0.166928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107013 restraints weight = 36116.350| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.15 r_work: 0.3302 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22460 Z= 0.236 Angle : 0.694 12.985 30384 Z= 0.349 Chirality : 0.045 0.332 3376 Planarity : 0.004 0.053 3832 Dihedral : 5.597 57.144 3016 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.65 % Allowed : 22.15 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2696 helix: 0.94 (0.12), residues: 1737 sheet: -1.38 (0.45), residues: 99 loop : -0.04 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 497 TYR 0.022 0.002 TYR B 492 PHE 0.038 0.002 PHE D 540 TRP 0.013 0.002 TRP B 693 HIS 0.007 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00557 (22460) covalent geometry : angle 0.69387 (30384) hydrogen bonds : bond 0.04604 ( 1341) hydrogen bonds : angle 4.87893 ( 3885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 330 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7922 (mmm160) cc_final: 0.6881 (mtm110) REVERT: A 96 ARG cc_start: 0.8094 (ptm160) cc_final: 0.6639 (tmt170) REVERT: A 124 GLN cc_start: 0.8322 (mt0) cc_final: 0.7664 (tt0) REVERT: A 146 MET cc_start: 0.7253 (mmt) cc_final: 0.6811 (mmt) REVERT: A 324 ASN cc_start: 0.7974 (m-40) cc_final: 0.7631 (m110) REVERT: A 377 TYR cc_start: 0.7687 (m-10) cc_final: 0.7481 (m-10) REVERT: A 420 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6664 (p) REVERT: A 516 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.3295 (tp) REVERT: A 527 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: A 676 MET cc_start: 0.8735 (mmt) cc_final: 0.8153 (mmt) REVERT: A 679 MET cc_start: 0.8697 (mtp) cc_final: 0.8338 (ptm) REVERT: B 64 TRP cc_start: 0.6808 (m100) cc_final: 0.6272 (m-10) REVERT: B 139 TYR cc_start: 0.8592 (t80) cc_final: 0.8275 (t80) REVERT: B 295 ASP cc_start: 0.8420 (t70) cc_final: 0.8067 (t0) REVERT: B 334 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7262 (mmtt) REVERT: B 421 ASP cc_start: 0.8430 (m-30) cc_final: 0.7942 (t0) REVERT: B 422 HIS cc_start: 0.8279 (m-70) cc_final: 0.7956 (m-70) REVERT: B 434 LEU cc_start: 0.7706 (mp) cc_final: 0.6942 (pp) REVERT: B 456 ASP cc_start: 0.8634 (p0) cc_final: 0.8127 (p0) REVERT: B 470 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7647 (ttp80) REVERT: B 482 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8473 (tptp) REVERT: B 492 TYR cc_start: 0.8505 (m-80) cc_final: 0.8288 (m-80) REVERT: B 504 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7591 (mmm) REVERT: B 652 MET cc_start: 0.7127 (tpp) cc_final: 0.6583 (mpp) REVERT: B 679 MET cc_start: 0.8154 (ptt) cc_final: 0.7781 (ptm) REVERT: C 121 ARG cc_start: 0.7449 (mtp85) cc_final: 0.6536 (tmt170) REVERT: C 205 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 317 GLU cc_start: 0.8349 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 337 ARG cc_start: 0.7166 (mtp85) cc_final: 0.6836 (mtp85) REVERT: C 362 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 371 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7909 (mttt) REVERT: C 493 PHE cc_start: 0.6279 (p90) cc_final: 0.5720 (p90) REVERT: C 494 HIS cc_start: 0.8120 (m-70) cc_final: 0.7902 (m-70) REVERT: C 562 TYR cc_start: 0.7414 (p90) cc_final: 0.7192 (p90) REVERT: C 601 LEU cc_start: 0.8899 (tp) cc_final: 0.8544 (pt) REVERT: C 626 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7567 (pp20) REVERT: C 627 ASP cc_start: 0.8209 (m-30) cc_final: 0.6930 (m-30) REVERT: C 655 ASN cc_start: 0.8747 (t0) cc_final: 0.8317 (p0) REVERT: C 661 HIS cc_start: 0.8771 (m-70) cc_final: 0.8450 (m90) REVERT: C 666 HIS cc_start: 0.7505 (m90) cc_final: 0.7016 (m-70) REVERT: C 676 MET cc_start: 0.7745 (mmp) cc_final: 0.7510 (mmp) REVERT: D 64 TRP cc_start: 0.6167 (t-100) cc_final: 0.5842 (t-100) REVERT: D 134 ARG cc_start: 0.7413 (mmm160) cc_final: 0.6807 (mmm160) REVERT: D 296 MET cc_start: 0.8589 (ttp) cc_final: 0.8385 (ttp) REVERT: D 301 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7591 (t80) REVERT: D 326 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 354 HIS cc_start: 0.6844 (t-90) cc_final: 0.6262 (m170) REVERT: D 388 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7722 (tmtt) REVERT: D 442 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 515 LYS cc_start: 0.4799 (OUTLIER) cc_final: 0.3953 (mppt) REVERT: D 700 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8448 (tp30) REVERT: D 709 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7963 (mt) outliers start: 111 outliers final: 92 residues processed: 415 average time/residue: 0.1364 time to fit residues: 89.5099 Evaluate side-chains 421 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 319 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 126 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.167611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108259 restraints weight = 36093.418| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.15 r_work: 0.3315 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22460 Z= 0.196 Angle : 0.689 12.640 30384 Z= 0.345 Chirality : 0.044 0.316 3376 Planarity : 0.004 0.056 3832 Dihedral : 5.524 55.912 3014 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.36 % Allowed : 22.74 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2696 helix: 0.91 (0.12), residues: 1744 sheet: -1.38 (0.45), residues: 99 loop : -0.06 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 497 TYR 0.023 0.002 TYR D 130 PHE 0.040 0.002 PHE D 540 TRP 0.013 0.001 TRP B 693 HIS 0.007 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00460 (22460) covalent geometry : angle 0.68923 (30384) hydrogen bonds : bond 0.04554 ( 1341) hydrogen bonds : angle 4.87542 ( 3885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 337 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7946 (mmm160) cc_final: 0.6878 (mtm110) REVERT: A 96 ARG cc_start: 0.8088 (ptm160) cc_final: 0.6662 (tmt170) REVERT: A 124 GLN cc_start: 0.8331 (mt0) cc_final: 0.7663 (tt0) REVERT: A 146 MET cc_start: 0.7210 (mmt) cc_final: 0.6780 (mmt) REVERT: A 324 ASN cc_start: 0.7937 (m-40) cc_final: 0.7581 (m110) REVERT: A 377 TYR cc_start: 0.7755 (m-10) cc_final: 0.7480 (m-10) REVERT: A 420 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6649 (p) REVERT: A 467 PHE cc_start: 0.8246 (p90) cc_final: 0.7525 (p90) REVERT: A 516 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.3310 (tp) REVERT: A 527 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: A 676 MET cc_start: 0.8727 (mmt) cc_final: 0.8249 (mmt) REVERT: A 679 MET cc_start: 0.8700 (mtp) cc_final: 0.8390 (ptp) REVERT: B 64 TRP cc_start: 0.6797 (m100) cc_final: 0.6338 (m-10) REVERT: B 139 TYR cc_start: 0.8568 (t80) cc_final: 0.8272 (t80) REVERT: B 295 ASP cc_start: 0.8417 (t70) cc_final: 0.8051 (t0) REVERT: B 334 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7269 (mmtt) REVERT: B 421 ASP cc_start: 0.8420 (m-30) cc_final: 0.7943 (t0) REVERT: B 422 HIS cc_start: 0.8268 (m-70) cc_final: 0.7945 (m-70) REVERT: B 434 LEU cc_start: 0.7706 (mp) cc_final: 0.7057 (pp) REVERT: B 456 ASP cc_start: 0.8620 (p0) cc_final: 0.8092 (p0) REVERT: B 482 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8441 (tptp) REVERT: B 492 TYR cc_start: 0.8510 (m-80) cc_final: 0.8217 (m-80) REVERT: B 495 ASP cc_start: 0.7588 (m-30) cc_final: 0.7375 (m-30) REVERT: B 652 MET cc_start: 0.7151 (tpp) cc_final: 0.6629 (mpp) REVERT: B 679 MET cc_start: 0.8206 (ptt) cc_final: 0.7916 (ptm) REVERT: C 78 TYR cc_start: 0.8676 (t80) cc_final: 0.8365 (t80) REVERT: C 121 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6528 (tmt170) REVERT: C 205 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 317 GLU cc_start: 0.8326 (tt0) cc_final: 0.7575 (tm-30) REVERT: C 337 ARG cc_start: 0.7160 (mtp85) cc_final: 0.6827 (mtp85) REVERT: C 362 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8250 (mm-40) REVERT: C 371 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7897 (mttt) REVERT: C 493 PHE cc_start: 0.6278 (p90) cc_final: 0.5716 (p90) REVERT: C 494 HIS cc_start: 0.8128 (m-70) cc_final: 0.7910 (m-70) REVERT: C 562 TYR cc_start: 0.7399 (p90) cc_final: 0.7169 (p90) REVERT: C 601 LEU cc_start: 0.8879 (tp) cc_final: 0.8562 (pt) REVERT: C 623 PHE cc_start: 0.6014 (m-80) cc_final: 0.5685 (m-10) REVERT: C 626 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7564 (pp20) REVERT: C 627 ASP cc_start: 0.8299 (m-30) cc_final: 0.7708 (m-30) REVERT: C 655 ASN cc_start: 0.8717 (t0) cc_final: 0.8299 (p0) REVERT: C 661 HIS cc_start: 0.8773 (m-70) cc_final: 0.8451 (m90) REVERT: C 666 HIS cc_start: 0.7499 (m90) cc_final: 0.6965 (m-70) REVERT: C 676 MET cc_start: 0.7702 (mmp) cc_final: 0.7285 (mmm) REVERT: D 64 TRP cc_start: 0.6146 (t-100) cc_final: 0.5809 (t-100) REVERT: D 301 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 325 ASP cc_start: 0.8141 (m-30) cc_final: 0.7904 (t0) REVERT: D 326 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7850 (mp) REVERT: D 354 HIS cc_start: 0.6821 (t-90) cc_final: 0.6328 (m170) REVERT: D 369 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8235 (ttm110) REVERT: D 388 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7733 (tmtt) REVERT: D 442 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7270 (mt-10) REVERT: D 515 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.3952 (mppt) REVERT: D 700 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8487 (tp30) REVERT: D 709 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7992 (mt) outliers start: 104 outliers final: 88 residues processed: 414 average time/residue: 0.1291 time to fit residues: 85.4634 Evaluate side-chains 421 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 324 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 TYR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 514 LYS Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 115 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 350 GLN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.165722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105457 restraints weight = 36133.585| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.15 r_work: 0.3269 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 22460 Z= 0.305 Angle : 0.760 13.279 30384 Z= 0.384 Chirality : 0.048 0.317 3376 Planarity : 0.004 0.049 3832 Dihedral : 5.559 56.213 3012 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.52 % Allowed : 22.86 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2696 helix: 0.74 (0.12), residues: 1737 sheet: -1.59 (0.44), residues: 99 loop : -0.09 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 497 TYR 0.029 0.002 TYR C 274 PHE 0.036 0.002 PHE D 540 TRP 0.013 0.002 TRP B 235 HIS 0.008 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00721 (22460) covalent geometry : angle 0.76026 (30384) hydrogen bonds : bond 0.04807 ( 1341) hydrogen bonds : angle 5.05035 ( 3885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7991.14 seconds wall clock time: 136 minutes 38.10 seconds (8198.10 seconds total)