Starting phenix.real_space_refine on Sat Feb 7 15:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dau_27276/02_2026/8dau_27276.map" } resolution = 3.7 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= -0.017 sd= 1.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 29 5.49 5 S 156 5.16 5 C 21438 2.51 5 N 5955 2.21 5 O 6668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34248 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5555 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5599 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 680} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4311 Classifications: {'peptide': 555} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 4 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4240 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 517} Chain breaks: 5 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4113 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4284 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 5 Chain: "G" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3825 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 453} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain breaks: 1 Chain: "I" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28365 SG CYS G 137 46.667 49.266 94.291 1.00108.38 S ATOM 28425 SG CYS G 145 50.351 49.983 94.351 1.00 88.12 S ATOM 28452 SG CYS G 148 48.238 50.081 97.410 1.00 87.79 S ATOM 28922 SG CYS G 204 74.888 91.352 115.516 1.00102.01 S ATOM 29020 SG CYS G 216 75.252 90.917 111.812 1.00 87.55 S ATOM 29041 SG CYS G 219 72.449 92.854 113.118 1.00 90.95 S Time building chain proxies: 7.26, per 1000 atoms: 0.21 Number of scatterers: 34248 At special positions: 0 Unit cell: (151.088, 169.176, 191.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 156 16.00 P 29 15.00 O 6668 8.00 N 5955 7.00 C 21438 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8124 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 24 sheets defined 53.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.604A pdb=" N MET A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.218A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 201 through 207 removed outlier: 3.771A pdb=" N GLU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 219 through 236 removed outlier: 4.344A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.573A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.708A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 removed outlier: 3.582A pdb=" N ARG A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.772A pdb=" N ARG A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.505A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 removed outlier: 4.389A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.605A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.386A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.850A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.504A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.585A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 621 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 718 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.730A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.539A pdb=" N MET B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.077A pdb=" N GLU B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 4.237A pdb=" N VAL B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 removed outlier: 4.808A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 282 through 285 removed outlier: 3.642A pdb=" N MET B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.579A pdb=" N ALA B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 395 Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 417 through 438 removed outlier: 4.040A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.502A pdb=" N PHE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.397A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.103A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 545 Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.101A pdb=" N ARG B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 718 Processing helix chain 'B' and resid 754 through 764 removed outlier: 3.818A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 786 Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.552A pdb=" N ARG C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 219 through 236 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 236 through 244 removed outlier: 4.451A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 290 through 305 Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.936A pdb=" N ILE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.643A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.575A pdb=" N ILE C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 413 removed outlier: 3.516A pdb=" N LEU C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.976A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.892A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 553 through 562 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 608 through 619 Processing helix chain 'C' and resid 640 through 645 removed outlier: 4.222A pdb=" N LEU C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 645 " --> pdb=" O PRO C 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 640 through 645' Processing helix chain 'C' and resid 659 through 671 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 693 through 718 Processing helix chain 'C' and resid 754 through 765 removed outlier: 3.862A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 786 removed outlier: 4.022A pdb=" N LEU C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 219 through 236 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 236 through 244 removed outlier: 4.363A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 288 through 306 Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.010A pdb=" N ILE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 405 through 413 Processing helix chain 'D' and resid 417 through 438 removed outlier: 3.970A pdb=" N ASP D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.769A pdb=" N GLU D 476 " --> pdb=" O ALA D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.771A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.519A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.216A pdb=" N MET D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 579 Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 608 through 620 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 659 through 671 Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 718 removed outlier: 3.923A pdb=" N LEU D 697 " --> pdb=" O SER D 693 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 removed outlier: 4.455A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 786 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 236 removed outlier: 3.760A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.967A pdb=" N VAL E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 removed outlier: 3.668A pdb=" N SER E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.017A pdb=" N ILE E 319 " --> pdb=" O GLU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 345 removed outlier: 3.879A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.572A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 455 removed outlier: 3.550A pdb=" N LEU E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 485 through 489 Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.229A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 509 through 516 Processing helix chain 'E' and resid 535 through 545 Processing helix chain 'E' and resid 553 through 563 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 593 Processing helix chain 'E' and resid 608 through 620 Processing helix chain 'E' and resid 635 through 639 Processing helix chain 'E' and resid 640 through 645 removed outlier: 3.880A pdb=" N ARG E 645 " --> pdb=" O ALA E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 672 Processing helix chain 'E' and resid 681 through 689 removed outlier: 3.923A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR E 689 " --> pdb=" O ILE E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 718 Processing helix chain 'E' and resid 754 through 764 removed outlier: 4.114A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 786 Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.601A pdb=" N ASN F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 3.915A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 236 through 244 removed outlier: 4.287A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 306 removed outlier: 3.753A pdb=" N SER F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 3.641A pdb=" N ILE F 319 " --> pdb=" O GLU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.841A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 369 removed outlier: 3.685A pdb=" N ARG F 369 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 417 through 438 removed outlier: 3.764A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 454 removed outlier: 3.562A pdb=" N LEU F 452 " --> pdb=" O ASP F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 485 through 489 removed outlier: 3.532A pdb=" N VAL F 489 " --> pdb=" O TRP F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.616A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 509 through 517 removed outlier: 4.058A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.632A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 563 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 593 removed outlier: 3.863A pdb=" N ILE F 592 " --> pdb=" O LEU F 589 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 593 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 621 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 659 through 671 Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 682 through 688 Processing helix chain 'F' and resid 693 through 718 Processing helix chain 'F' and resid 754 through 764 removed outlier: 3.550A pdb=" N PHE F 758 " --> pdb=" O THR F 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 786 removed outlier: 3.539A pdb=" N LEU F 774 " --> pdb=" O SER F 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 removed outlier: 3.582A pdb=" N GLU G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 removed outlier: 3.821A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 181 removed outlier: 4.078A pdb=" N SER G 171 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 254 removed outlier: 4.322A pdb=" N ILE G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.776A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 402 through 412 removed outlier: 3.826A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 513 Processing helix chain 'G' and resid 516 through 524 Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.613A pdb=" N GLN G 537 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 555 through 566 removed outlier: 4.140A pdb=" N SER G 559 " --> pdb=" O GLU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.554A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 254 removed outlier: 3.754A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 155 through 160 removed outlier: 3.775A pdb=" N TYR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.851A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 239 No H-bonds generated for 'chain 'K' and resid 237 through 239' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.193A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.766A pdb=" N ARG A 154 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 280 removed outlier: 6.349A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 357 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 250 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 552 removed outlier: 6.824A pdb=" N GLY A 523 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 120 removed outlier: 7.312A pdb=" N LYS B 119 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.042A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 280 removed outlier: 6.497A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.443A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.429A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 357 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 524 through 527 Processing sheet with id=AB4, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AB5, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.511A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 357 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY D 250 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL D 377 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 252 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 548 through 553 removed outlier: 6.798A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 275 through 279 removed outlier: 3.545A pdb=" N MET E 253 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 548 through 552 removed outlier: 3.830A pdb=" N VAL E 583 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL E 524 " --> pdb=" O VAL E 629 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 275 through 278 removed outlier: 7.047A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 548 through 552 removed outlier: 3.585A pdb=" N VAL F 524 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY F 523 " --> pdb=" O GLN F 651 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE F 653 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 525 " --> pdb=" O ILE F 653 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 463 through 465 removed outlier: 6.285A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG G 259 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS G 236 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL G 281 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU G 238 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA G 283 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 469 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G 239 " --> pdb=" O GLY G 469 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 422 through 424 Processing sheet with id=AC4, first strand: chain 'G' and resid 441 through 442 removed outlier: 3.505A pdb=" N VAL G 449 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 113 through 116 removed outlier: 3.539A pdb=" N LEU J 169 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 215 removed outlier: 6.544A pdb=" N PHE K 204 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU K 269 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS K 206 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU K 271 " --> pdb=" O LYS K 206 " (cutoff:3.500A) 1598 hydrogen bonds defined for protein. 4506 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: 6.36 Time building geometry restraints manager: 3.72 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: 11581 1.34 - 1.46: 6344 1.46 - 1.58: 16565 1.58 - 1.70: 41 1.70 - 1.81: 288 Bond restraints: 34819 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 34814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.67: 46846 5.67 - 11.35: 222 11.35 - 17.02: 37 17.02 - 22.70: 5 22.70 - 28.37: 1 Bond angle restraints: 47111 Sorted by residual: angle pdb=" C ARG B 672 " pdb=" N LYS B 673 " pdb=" CA LYS B 673 " ideal model delta sigma weight residual 120.29 137.43 -17.14 1.42e+00 4.96e-01 1.46e+02 angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 150.17 -28.37 2.44e+00 1.68e-01 1.35e+02 angle pdb=" C PRO E 248 " pdb=" N ARG E 249 " pdb=" CA ARG E 249 " ideal model delta sigma weight residual 122.58 144.72 -22.14 2.07e+00 2.33e-01 1.14e+02 angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 121.54 141.02 -19.48 1.91e+00 2.74e-01 1.04e+02 angle pdb=" C ILE B 94 " pdb=" N ASN B 95 " pdb=" CA ASN B 95 " ideal model delta sigma weight residual 121.06 139.86 -18.80 1.88e+00 2.83e-01 1.00e+02 ... (remaining 47106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 21269 33.12 - 66.24: 234 66.24 - 99.36: 26 99.36 - 132.48: 15 132.48 - 165.60: 4 Dihedral angle restraints: 21548 sinusoidal: 9006 harmonic: 12542 Sorted by residual: dihedral pdb=" CA ALA F 307 " pdb=" C ALA F 307 " pdb=" N PRO F 308 " pdb=" CA PRO F 308 " ideal model delta harmonic sigma weight residual 180.00 137.48 42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -102.85 -165.60 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual 300.00 153.20 146.81 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 21545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 5166 0.344 - 0.688: 76 0.688 - 1.033: 0 1.033 - 1.377: 5 1.377 - 1.721: 59 Chirality restraints: 5306 Sorted by residual: chirality pdb=" CG LEU E 367 " pdb=" CB LEU E 367 " pdb=" CD1 LEU E 367 " pdb=" CD2 LEU E 367 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU E 586 " pdb=" CB LEU E 586 " pdb=" CD1 LEU E 586 " pdb=" CD2 LEU E 586 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 ... (remaining 5303 not shown) Planarity restraints: 6138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C GLU B 329 " -0.032 2.00e-02 2.50e+03 pdb=" O GLU B 329 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL B 330 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 294 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C SER F 294 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 294 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN F 295 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 506 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C LYS G 506 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR G 507 " 0.009 2.00e-02 2.50e+03 ... (remaining 6135 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 384 2.52 - 3.11: 28884 3.11 - 3.71: 52807 3.71 - 4.30: 69788 4.30 - 4.90: 117919 Nonbonded interactions: 269782 Sorted by model distance: nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.924 3.040 nonbonded pdb=" OG SER D 559 " pdb=" O GLU D 564 " model vdw 1.925 3.040 nonbonded pdb=" OD1 ASP B 590 " pdb=" OG1 THR B 633 " model vdw 1.954 3.040 nonbonded pdb=" OG SER G 351 " pdb=" OE1 GLU G 354 " model vdw 1.967 3.040 nonbonded pdb=" OG1 THR C 262 " pdb=" O1G ATP C 901 " model vdw 1.981 3.040 ... (remaining 269777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 440 or resid 447 through 902)) selection = (chain 'B' and resid 33 through 902) } ncs_group { reference = (chain 'C' and (resid 207 through 440 or resid 447 through 786 or resid 902)) selection = (chain 'D' and (resid 207 through 786 or resid 902)) selection = (chain 'E' and (resid 207 through 786 or resid 902)) selection = (chain 'F' and (resid 207 through 786 or resid 902)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.600 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 34829 Z= 0.170 Angle : 0.930 28.372 47117 Z= 0.471 Chirality : 0.184 1.721 5306 Planarity : 0.003 0.036 6138 Dihedral : 11.503 165.603 13424 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 0.90 % Allowed : 4.51 % Favored : 94.59 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.14), residues: 4274 helix: 2.39 (0.12), residues: 2004 sheet: 0.13 (0.23), residues: 530 loop : -0.03 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.020 0.001 TYR G 507 PHE 0.009 0.001 PHE C 275 TRP 0.006 0.001 TRP G 489 HIS 0.004 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00349 (34819) covalent geometry : angle 0.92981 (47111) hydrogen bonds : bond 0.14428 ( 1598) hydrogen bonds : angle 5.33908 ( 4506) metal coordination : bond 0.06701 ( 8) metal coordination : angle 3.06690 ( 6) Misc. bond : bond 0.05822 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 591 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.6283 (mm) cc_final: 0.5926 (mm) REVERT: A 151 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8734 (mm-30) REVERT: A 194 TRP cc_start: 0.1698 (p90) cc_final: 0.0334 (t60) REVERT: A 208 MET cc_start: 0.8145 (tmm) cc_final: 0.7929 (tmm) REVERT: A 405 ASP cc_start: 0.8347 (t70) cc_final: 0.8091 (t0) REVERT: B 65 ASP cc_start: 0.4621 (OUTLIER) cc_final: 0.3981 (m-30) REVERT: B 183 TYR cc_start: 0.7170 (p90) cc_final: 0.6779 (p90) REVERT: B 332 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6280 (mtt180) REVERT: B 483 ASN cc_start: 0.8564 (t0) cc_final: 0.8267 (p0) REVERT: B 588 GLU cc_start: 0.8363 (tt0) cc_final: 0.8058 (tm-30) REVERT: B 778 GLU cc_start: 0.8511 (mp0) cc_final: 0.8232 (mm-30) REVERT: C 317 ASP cc_start: 0.7908 (p0) cc_final: 0.7633 (t0) REVERT: C 342 MET cc_start: 0.8525 (tpp) cc_final: 0.8131 (mmm) REVERT: C 348 ARG cc_start: 0.8586 (mtt90) cc_final: 0.7597 (mmm160) REVERT: C 561 TRP cc_start: 0.6281 (t60) cc_final: 0.6028 (t60) REVERT: C 570 ARG cc_start: 0.8219 (mmm160) cc_final: 0.6966 (tpp80) REVERT: C 608 ASP cc_start: 0.5783 (m-30) cc_final: 0.5575 (m-30) REVERT: C 649 LEU cc_start: 0.9076 (mm) cc_final: 0.8749 (tp) REVERT: D 402 ASP cc_start: 0.7841 (m-30) cc_final: 0.7558 (p0) REVERT: E 409 LEU cc_start: 0.9163 (mt) cc_final: 0.8465 (mt) REVERT: E 430 MET cc_start: 0.8180 (tpp) cc_final: 0.7901 (ttp) REVERT: E 560 MET cc_start: 0.5852 (mpp) cc_final: 0.5484 (mpp) REVERT: E 614 LEU cc_start: 0.8664 (tt) cc_final: 0.8409 (pp) REVERT: E 699 TYR cc_start: 0.7710 (t80) cc_final: 0.7500 (t80) REVERT: E 784 MET cc_start: 0.7336 (mmp) cc_final: 0.7007 (mtp) REVERT: F 287 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7373 (mmtp) REVERT: F 359 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8400 (ttm110) REVERT: F 483 ASN cc_start: 0.7671 (p0) cc_final: 0.7286 (t0) REVERT: F 588 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8633 (mt-10) REVERT: F 621 MET cc_start: 0.8035 (ppp) cc_final: 0.7819 (ppp) REVERT: G 133 LYS cc_start: 0.8638 (tmtt) cc_final: 0.8155 (tttt) REVERT: G 218 LYS cc_start: 0.8767 (ptmt) cc_final: 0.8334 (ptmt) REVERT: G 387 SER cc_start: 0.8540 (p) cc_final: 0.8202 (t) REVERT: G 455 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7817 (Cg_exo) REVERT: G 548 ILE cc_start: 0.9172 (pt) cc_final: 0.8931 (pt) REVERT: I 29 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8634 (ttpp) outliers start: 33 outliers final: 12 residues processed: 614 average time/residue: 0.2618 time to fit residues: 243.7069 Evaluate side-chains 323 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 310 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 225 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 113 HIS A 225 GLN A 394 HIS A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 394 HIS D 702 GLN ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 394 HIS G 106 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 528 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.116721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085826 restraints weight = 110320.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086659 restraints weight = 59500.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086805 restraints weight = 41343.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087235 restraints weight = 39307.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087257 restraints weight = 34355.036| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34829 Z= 0.165 Angle : 0.668 9.265 47117 Z= 0.326 Chirality : 0.045 0.224 5306 Planarity : 0.004 0.046 6138 Dihedral : 11.099 155.679 4957 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 1.93 % Allowed : 9.13 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4274 helix: 1.91 (0.12), residues: 2019 sheet: -0.03 (0.23), residues: 552 loop : -0.09 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 475 TYR 0.023 0.001 TYR G 507 PHE 0.015 0.002 PHE G 260 TRP 0.007 0.001 TRP B 486 HIS 0.027 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00376 (34819) covalent geometry : angle 0.66651 (47111) hydrogen bonds : bond 0.03981 ( 1598) hydrogen bonds : angle 4.64417 ( 4506) metal coordination : bond 0.01167 ( 8) metal coordination : angle 3.31374 ( 6) Misc. bond : bond 0.00299 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 1.422 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 60 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7138 (pm20) REVERT: A 151 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8719 (tp30) REVERT: A 194 TRP cc_start: 0.1794 (p90) cc_final: 0.0418 (t60) REVERT: A 229 MET cc_start: 0.8642 (mtt) cc_final: 0.8396 (mtt) REVERT: A 283 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 65 ASP cc_start: 0.4177 (OUTLIER) cc_final: 0.2553 (m-30) REVERT: B 86 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: B 183 TYR cc_start: 0.7116 (p90) cc_final: 0.6867 (p90) REVERT: B 315 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7965 (mm-30) REVERT: B 332 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6389 (mpp80) REVERT: B 483 ASN cc_start: 0.8548 (t0) cc_final: 0.8103 (p0) REVERT: B 560 MET cc_start: 0.7379 (mtt) cc_final: 0.7053 (tpt) REVERT: B 588 GLU cc_start: 0.8411 (tt0) cc_final: 0.7933 (tm-30) REVERT: B 778 GLU cc_start: 0.8472 (mp0) cc_final: 0.8249 (mm-30) REVERT: C 317 ASP cc_start: 0.7784 (p0) cc_final: 0.7491 (t0) REVERT: C 342 MET cc_start: 0.8643 (tpp) cc_final: 0.8177 (mmm) REVERT: C 570 ARG cc_start: 0.8185 (mmm160) cc_final: 0.6939 (tpp80) REVERT: C 649 LEU cc_start: 0.8966 (mm) cc_final: 0.8672 (tp) REVERT: D 314 ASP cc_start: 0.8226 (t0) cc_final: 0.7973 (t0) REVERT: D 331 GLU cc_start: 0.8398 (mp0) cc_final: 0.8044 (mp0) REVERT: D 402 ASP cc_start: 0.8239 (m-30) cc_final: 0.7824 (p0) REVERT: E 288 MET cc_start: 0.7003 (mmm) cc_final: 0.6478 (mmm) REVERT: E 430 MET cc_start: 0.8137 (tpp) cc_final: 0.7780 (ttp) REVERT: E 500 LYS cc_start: 0.7035 (mttt) cc_final: 0.6737 (ptpt) REVERT: E 614 LEU cc_start: 0.8770 (tt) cc_final: 0.8459 (pp) REVERT: E 784 MET cc_start: 0.7520 (mmp) cc_final: 0.7104 (mtp) REVERT: F 359 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8480 (ttm110) REVERT: F 483 ASN cc_start: 0.7674 (p0) cc_final: 0.7258 (t0) REVERT: F 556 GLU cc_start: 0.8753 (mp0) cc_final: 0.8278 (mp0) REVERT: F 587 ASP cc_start: 0.8447 (t0) cc_final: 0.8178 (t0) REVERT: F 588 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8638 (mt-10) REVERT: G 126 ASP cc_start: 0.8486 (p0) cc_final: 0.8270 (p0) REVERT: G 387 SER cc_start: 0.8545 (p) cc_final: 0.8285 (t) REVERT: G 422 MET cc_start: 0.8485 (mmm) cc_final: 0.8166 (mmm) REVERT: G 548 ILE cc_start: 0.9012 (pt) cc_final: 0.8719 (pt) REVERT: H 288 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7618 (mt-10) REVERT: I 29 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8705 (ttpp) outliers start: 71 outliers final: 33 residues processed: 399 average time/residue: 0.2331 time to fit residues: 149.5358 Evaluate side-chains 317 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 234 optimal weight: 3.9990 chunk 410 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 422 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 396 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** G 208 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.115799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084565 restraints weight = 110101.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085418 restraints weight = 58243.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085760 restraints weight = 41528.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086012 restraints weight = 38881.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.086066 restraints weight = 33744.460| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34829 Z= 0.175 Angle : 0.635 9.511 47117 Z= 0.309 Chirality : 0.044 0.196 5306 Planarity : 0.004 0.048 6138 Dihedral : 10.626 147.605 4943 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 2.28 % Allowed : 10.60 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4274 helix: 1.73 (0.12), residues: 2030 sheet: -0.01 (0.22), residues: 572 loop : -0.15 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.024 0.001 TYR C 254 PHE 0.014 0.001 PHE G 381 TRP 0.007 0.001 TRP G 252 HIS 0.015 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00404 (34819) covalent geometry : angle 0.63419 (47111) hydrogen bonds : bond 0.03674 ( 1598) hydrogen bonds : angle 4.54510 ( 4506) metal coordination : bond 0.01045 ( 8) metal coordination : angle 3.06195 ( 6) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 305 time to evaluate : 1.368 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 56 MET cc_start: 0.6648 (ttp) cc_final: 0.6157 (tmm) REVERT: A 60 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7411 (pm20) REVERT: A 194 TRP cc_start: 0.1789 (p90) cc_final: 0.0381 (t60) REVERT: A 208 MET cc_start: 0.8790 (tmm) cc_final: 0.8111 (tmm) REVERT: A 266 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7364 (mmm160) REVERT: B 86 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 151 GLU cc_start: 0.7383 (mp0) cc_final: 0.5856 (tm-30) REVERT: B 183 TYR cc_start: 0.7248 (p90) cc_final: 0.6980 (p90) REVERT: B 315 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8131 (mm-30) REVERT: B 483 ASN cc_start: 0.8525 (t0) cc_final: 0.8111 (p0) REVERT: B 762 MET cc_start: 0.6725 (ptt) cc_final: 0.6515 (ptt) REVERT: B 778 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: C 317 ASP cc_start: 0.7844 (p0) cc_final: 0.7560 (t0) REVERT: C 342 MET cc_start: 0.8696 (tpp) cc_final: 0.8147 (mmm) REVERT: C 348 ARG cc_start: 0.8527 (mtt90) cc_final: 0.7625 (mmm160) REVERT: C 570 ARG cc_start: 0.8221 (mmm160) cc_final: 0.6885 (tpp80) REVERT: C 699 TYR cc_start: 0.8646 (t80) cc_final: 0.8012 (m-80) REVERT: D 223 MET cc_start: 0.9094 (tpp) cc_final: 0.8332 (mmm) REVERT: D 331 GLU cc_start: 0.8355 (mp0) cc_final: 0.8013 (mp0) REVERT: D 402 ASP cc_start: 0.8270 (m-30) cc_final: 0.7813 (p0) REVERT: D 587 ASP cc_start: 0.6875 (m-30) cc_final: 0.6600 (m-30) REVERT: E 285 MET cc_start: 0.7256 (mmp) cc_final: 0.6933 (mmp) REVERT: E 430 MET cc_start: 0.8216 (tpp) cc_final: 0.7809 (ttp) REVERT: E 614 LEU cc_start: 0.8910 (tt) cc_final: 0.8578 (pp) REVERT: E 784 MET cc_start: 0.7539 (mmp) cc_final: 0.7175 (mtp) REVERT: F 359 ARG cc_start: 0.8789 (tpp80) cc_final: 0.8494 (ttm110) REVERT: F 483 ASN cc_start: 0.7680 (p0) cc_final: 0.7215 (t0) REVERT: F 556 GLU cc_start: 0.8716 (mp0) cc_final: 0.8312 (mp0) REVERT: F 587 ASP cc_start: 0.8450 (t0) cc_final: 0.8130 (t0) REVERT: F 588 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8670 (mt-10) REVERT: F 618 MET cc_start: 0.8848 (tpt) cc_final: 0.8632 (tpt) REVERT: F 699 TYR cc_start: 0.9011 (t80) cc_final: 0.8767 (t80) REVERT: G 387 SER cc_start: 0.8636 (p) cc_final: 0.8317 (t) REVERT: H 232 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8345 (p) REVERT: I 29 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8746 (ttpp) outliers start: 84 outliers final: 43 residues processed: 367 average time/residue: 0.2160 time to fit residues: 128.3670 Evaluate side-chains 319 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 363 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 157 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS C 612 ASN ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.116587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085266 restraints weight = 109351.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086657 restraints weight = 60096.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086706 restraints weight = 40139.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087182 restraints weight = 38778.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087193 restraints weight = 33584.010| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34829 Z= 0.161 Angle : 0.618 8.594 47117 Z= 0.300 Chirality : 0.043 0.192 5306 Planarity : 0.004 0.050 6138 Dihedral : 10.254 143.502 4940 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 2.34 % Allowed : 11.82 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4274 helix: 1.71 (0.12), residues: 2024 sheet: -0.04 (0.22), residues: 572 loop : -0.22 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 475 TYR 0.023 0.001 TYR C 254 PHE 0.018 0.001 PHE D 628 TRP 0.006 0.001 TRP B 486 HIS 0.015 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00371 (34819) covalent geometry : angle 0.61721 (47111) hydrogen bonds : bond 0.03439 ( 1598) hydrogen bonds : angle 4.47643 ( 4506) metal coordination : bond 0.00964 ( 8) metal coordination : angle 2.98974 ( 6) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 284 time to evaluate : 1.429 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 56 MET cc_start: 0.6684 (ttp) cc_final: 0.6155 (tmm) REVERT: A 60 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7507 (pm20) REVERT: A 194 TRP cc_start: 0.1822 (p90) cc_final: 0.0836 (t60) REVERT: A 208 MET cc_start: 0.8691 (tmm) cc_final: 0.8463 (tmm) REVERT: A 254 TYR cc_start: 0.8714 (p90) cc_final: 0.8192 (p90) REVERT: B 86 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: B 168 MET cc_start: 0.6075 (tpp) cc_final: 0.5703 (ttm) REVERT: B 183 TYR cc_start: 0.7378 (p90) cc_final: 0.7096 (p90) REVERT: B 315 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8223 (mm-30) REVERT: B 483 ASN cc_start: 0.8538 (t0) cc_final: 0.8048 (p0) REVERT: B 556 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8177 (mp0) REVERT: C 317 ASP cc_start: 0.7831 (p0) cc_final: 0.7558 (t0) REVERT: C 342 MET cc_start: 0.8648 (tpp) cc_final: 0.8063 (mmm) REVERT: C 348 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8225 (mtt180) REVERT: C 475 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7909 (ptp-110) REVERT: C 570 ARG cc_start: 0.8326 (mmm160) cc_final: 0.6906 (tpp80) REVERT: C 618 MET cc_start: 0.7532 (tmm) cc_final: 0.7268 (tmm) REVERT: C 621 MET cc_start: 0.5969 (pmm) cc_final: 0.4813 (ptp) REVERT: C 699 TYR cc_start: 0.8648 (t80) cc_final: 0.7992 (m-80) REVERT: D 402 ASP cc_start: 0.8295 (m-30) cc_final: 0.7817 (p0) REVERT: E 430 MET cc_start: 0.8239 (tpp) cc_final: 0.7866 (ttp) REVERT: E 614 LEU cc_start: 0.8876 (tt) cc_final: 0.8559 (pp) REVERT: E 784 MET cc_start: 0.7574 (mmp) cc_final: 0.7168 (mtp) REVERT: F 323 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8237 (mmm-85) REVERT: F 359 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8429 (ttm110) REVERT: F 483 ASN cc_start: 0.7641 (p0) cc_final: 0.7141 (t0) REVERT: F 556 GLU cc_start: 0.8682 (mp0) cc_final: 0.8292 (mp0) REVERT: F 587 ASP cc_start: 0.8495 (t0) cc_final: 0.8152 (t0) REVERT: F 588 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8686 (mt-10) REVERT: F 618 MET cc_start: 0.8900 (tpt) cc_final: 0.8432 (tpt) REVERT: G 387 SER cc_start: 0.8620 (p) cc_final: 0.8295 (t) REVERT: G 422 MET cc_start: 0.8539 (mmm) cc_final: 0.8164 (mmm) REVERT: H 232 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8316 (p) REVERT: H 288 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7719 (mt-10) REVERT: I 29 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8730 (ttpp) outliers start: 86 outliers final: 58 residues processed: 348 average time/residue: 0.2090 time to fit residues: 118.8293 Evaluate side-chains 320 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 405 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 268 optimal weight: 0.0370 chunk 189 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN F 207 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.115967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084703 restraints weight = 109967.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085542 restraints weight = 58407.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085953 restraints weight = 40620.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086170 restraints weight = 39682.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086269 restraints weight = 33679.551| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34829 Z= 0.148 Angle : 0.605 8.292 47117 Z= 0.293 Chirality : 0.043 0.210 5306 Planarity : 0.004 0.049 6138 Dihedral : 9.915 139.102 4940 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 2.45 % Allowed : 12.69 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.13), residues: 4274 helix: 1.74 (0.12), residues: 2030 sheet: -0.06 (0.22), residues: 572 loop : -0.23 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 359 TYR 0.031 0.001 TYR A 513 PHE 0.013 0.001 PHE G 260 TRP 0.007 0.001 TRP G 252 HIS 0.008 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00339 (34819) covalent geometry : angle 0.60439 (47111) hydrogen bonds : bond 0.03301 ( 1598) hydrogen bonds : angle 4.38023 ( 4506) metal coordination : bond 0.00785 ( 8) metal coordination : angle 3.14274 ( 6) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 283 time to evaluate : 1.338 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 56 MET cc_start: 0.6711 (ttp) cc_final: 0.6177 (tmm) REVERT: A 60 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7474 (pm20) REVERT: A 112 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8083 (tp) REVERT: A 194 TRP cc_start: 0.1946 (p90) cc_final: 0.1054 (t60) REVERT: A 208 MET cc_start: 0.8737 (tmm) cc_final: 0.8481 (tmm) REVERT: B 86 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: B 151 GLU cc_start: 0.7345 (mp0) cc_final: 0.5840 (tm-30) REVERT: B 183 TYR cc_start: 0.7390 (p90) cc_final: 0.7062 (p90) REVERT: B 254 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7815 (p90) REVERT: B 315 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8300 (mm-30) REVERT: B 332 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: B 483 ASN cc_start: 0.8513 (t0) cc_final: 0.8038 (p0) REVERT: C 317 ASP cc_start: 0.7800 (p0) cc_final: 0.7591 (t0) REVERT: C 342 MET cc_start: 0.8655 (tpp) cc_final: 0.8061 (mmm) REVERT: C 348 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8204 (mtt180) REVERT: C 475 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7863 (ptp-110) REVERT: C 618 MET cc_start: 0.7594 (tmm) cc_final: 0.7339 (tmm) REVERT: C 621 MET cc_start: 0.6049 (pmm) cc_final: 0.4919 (ptp) REVERT: C 762 MET cc_start: 0.5878 (tmm) cc_final: 0.5547 (ptt) REVERT: D 402 ASP cc_start: 0.8243 (m-30) cc_final: 0.7756 (p0) REVERT: D 553 LYS cc_start: 0.7892 (tppt) cc_final: 0.7565 (tppt) REVERT: D 587 ASP cc_start: 0.7466 (t0) cc_final: 0.6750 (t0) REVERT: E 285 MET cc_start: 0.7275 (mmp) cc_final: 0.6300 (mmp) REVERT: E 288 MET cc_start: 0.7397 (mmt) cc_final: 0.7194 (mmm) REVERT: E 345 MET cc_start: 0.8119 (ttm) cc_final: 0.7896 (ttm) REVERT: E 430 MET cc_start: 0.8244 (tpp) cc_final: 0.7890 (ttp) REVERT: E 614 LEU cc_start: 0.8874 (tt) cc_final: 0.8578 (pp) REVERT: E 784 MET cc_start: 0.7522 (mmp) cc_final: 0.7141 (mtp) REVERT: F 287 LYS cc_start: 0.7271 (mmtm) cc_final: 0.7060 (mmtp) REVERT: F 359 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8366 (ttm110) REVERT: F 483 ASN cc_start: 0.7623 (p0) cc_final: 0.7136 (t0) REVERT: F 556 GLU cc_start: 0.8704 (mp0) cc_final: 0.8308 (mp0) REVERT: F 587 ASP cc_start: 0.8522 (t0) cc_final: 0.8159 (t0) REVERT: F 588 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8687 (mt-10) REVERT: F 699 TYR cc_start: 0.8997 (t80) cc_final: 0.8785 (t80) REVERT: G 112 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7418 (ptm160) REVERT: G 133 LYS cc_start: 0.9179 (mppt) cc_final: 0.8599 (tptp) REVERT: G 387 SER cc_start: 0.8599 (p) cc_final: 0.8282 (t) REVERT: H 232 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8255 (p) REVERT: H 288 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7610 (mt-10) REVERT: I 29 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8731 (ttpp) outliers start: 90 outliers final: 66 residues processed: 349 average time/residue: 0.2079 time to fit residues: 119.6204 Evaluate side-chains 339 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 140 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 176 optimal weight: 0.0570 chunk 328 optimal weight: 3.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.116667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.085604 restraints weight = 109878.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086560 restraints weight = 58280.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086955 restraints weight = 40259.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087173 restraints weight = 39324.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087267 restraints weight = 33354.252| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34829 Z= 0.119 Angle : 0.600 9.486 47117 Z= 0.286 Chirality : 0.042 0.206 5306 Planarity : 0.004 0.045 6138 Dihedral : 9.536 136.487 4938 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 2.39 % Allowed : 12.99 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4274 helix: 1.77 (0.12), residues: 2030 sheet: -0.03 (0.22), residues: 564 loop : -0.20 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 359 TYR 0.026 0.001 TYR C 254 PHE 0.013 0.001 PHE A 373 TRP 0.010 0.001 TRP D 561 HIS 0.004 0.001 HIS G 170 Details of bonding type rmsd covalent geometry : bond 0.00268 (34819) covalent geometry : angle 0.59895 (47111) hydrogen bonds : bond 0.03090 ( 1598) hydrogen bonds : angle 4.29299 ( 4506) metal coordination : bond 0.00580 ( 8) metal coordination : angle 2.59332 ( 6) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 1.297 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 MET cc_start: 0.6916 (ttp) cc_final: 0.6438 (tmm) REVERT: A 60 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7496 (pm20) REVERT: A 112 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8060 (tp) REVERT: A 194 TRP cc_start: 0.1896 (p90) cc_final: 0.1036 (t60) REVERT: A 208 MET cc_start: 0.8737 (tmm) cc_final: 0.8459 (tmm) REVERT: A 254 TYR cc_start: 0.8681 (p90) cc_final: 0.8124 (p90) REVERT: B 86 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: B 151 GLU cc_start: 0.7477 (mp0) cc_final: 0.5953 (tm-30) REVERT: B 183 TYR cc_start: 0.7453 (p90) cc_final: 0.7095 (p90) REVERT: B 315 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8253 (mm-30) REVERT: B 332 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6927 (mtm-85) REVERT: B 483 ASN cc_start: 0.8494 (t0) cc_final: 0.8042 (p0) REVERT: C 342 MET cc_start: 0.8532 (tpp) cc_final: 0.8024 (mmm) REVERT: C 348 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8248 (mtt180) REVERT: C 475 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7811 (ptp-110) REVERT: C 618 MET cc_start: 0.7595 (tmm) cc_final: 0.7369 (tmm) REVERT: C 621 MET cc_start: 0.6013 (pmm) cc_final: 0.4991 (ptp) REVERT: C 762 MET cc_start: 0.5847 (tmm) cc_final: 0.5559 (ptt) REVERT: D 402 ASP cc_start: 0.8229 (m-30) cc_final: 0.7726 (p0) REVERT: D 553 LYS cc_start: 0.7846 (tppt) cc_final: 0.7521 (tppt) REVERT: D 587 ASP cc_start: 0.7360 (t0) cc_final: 0.6671 (t0) REVERT: D 618 MET cc_start: 0.7848 (ttm) cc_final: 0.7541 (ptm) REVERT: D 645 ARG cc_start: 0.6640 (mtt-85) cc_final: 0.6375 (mtt-85) REVERT: E 285 MET cc_start: 0.7212 (mmp) cc_final: 0.6168 (mmp) REVERT: E 345 MET cc_start: 0.8131 (ttm) cc_final: 0.7897 (ttm) REVERT: E 430 MET cc_start: 0.8231 (tpp) cc_final: 0.7873 (ttp) REVERT: E 614 LEU cc_start: 0.8850 (tt) cc_final: 0.8559 (pp) REVERT: E 784 MET cc_start: 0.7513 (mmp) cc_final: 0.7131 (mtp) REVERT: F 359 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8349 (ttm110) REVERT: F 483 ASN cc_start: 0.7584 (p0) cc_final: 0.7066 (t0) REVERT: F 556 GLU cc_start: 0.8664 (mp0) cc_final: 0.8256 (mp0) REVERT: F 564 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7622 (pt0) REVERT: F 587 ASP cc_start: 0.8507 (t0) cc_final: 0.8156 (t0) REVERT: F 588 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8717 (mt-10) REVERT: F 621 MET cc_start: 0.8115 (ppp) cc_final: 0.7895 (ppp) REVERT: F 673 LYS cc_start: 0.7941 (tptm) cc_final: 0.7708 (tppp) REVERT: F 699 TYR cc_start: 0.8996 (t80) cc_final: 0.8753 (t80) REVERT: G 112 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7282 (ptm160) REVERT: G 147 TYR cc_start: 0.8655 (m-80) cc_final: 0.8350 (m-10) REVERT: G 387 SER cc_start: 0.8563 (p) cc_final: 0.8268 (t) REVERT: H 232 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8351 (p) REVERT: H 288 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7550 (mt-10) REVERT: I 29 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8732 (ttpp) outliers start: 88 outliers final: 68 residues processed: 351 average time/residue: 0.2129 time to fit residues: 124.0367 Evaluate side-chains 344 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 299 optimal weight: 10.0000 chunk 409 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN G 205 HIS ** G 208 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087359 restraints weight = 110181.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087233 restraints weight = 61827.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087571 restraints weight = 46999.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087874 restraints weight = 40568.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088011 restraints weight = 36511.195| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34829 Z= 0.123 Angle : 0.596 11.687 47117 Z= 0.285 Chirality : 0.042 0.251 5306 Planarity : 0.003 0.045 6138 Dihedral : 9.269 143.097 4938 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 2.34 % Allowed : 13.37 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4274 helix: 1.78 (0.12), residues: 2030 sheet: -0.05 (0.22), residues: 566 loop : -0.18 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 359 TYR 0.027 0.001 TYR C 254 PHE 0.011 0.001 PHE G 260 TRP 0.015 0.001 TRP D 561 HIS 0.006 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (34819) covalent geometry : angle 0.59536 (47111) hydrogen bonds : bond 0.03035 ( 1598) hydrogen bonds : angle 4.25543 ( 4506) metal coordination : bond 0.00595 ( 8) metal coordination : angle 2.79355 ( 6) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 291 time to evaluate : 1.486 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 56 MET cc_start: 0.7112 (ttp) cc_final: 0.6908 (tmm) REVERT: A 60 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7508 (pm20) REVERT: A 112 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 194 TRP cc_start: 0.1864 (p90) cc_final: 0.1040 (t60) REVERT: A 208 MET cc_start: 0.8728 (tmm) cc_final: 0.8430 (tmm) REVERT: A 254 TYR cc_start: 0.8686 (p90) cc_final: 0.8165 (p90) REVERT: B 183 TYR cc_start: 0.7396 (p90) cc_final: 0.7031 (p90) REVERT: B 254 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7853 (p90) REVERT: B 315 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8263 (mm-30) REVERT: B 332 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6966 (mtm-85) REVERT: B 483 ASN cc_start: 0.8496 (t0) cc_final: 0.8035 (p0) REVERT: B 556 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8306 (mp0) REVERT: C 348 ARG cc_start: 0.8612 (mtt90) cc_final: 0.7638 (mmm160) REVERT: C 370 PHE cc_start: 0.8575 (t80) cc_final: 0.8326 (t80) REVERT: C 475 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7844 (ptp-110) REVERT: C 570 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7129 (tpp80) REVERT: C 618 MET cc_start: 0.7638 (tmm) cc_final: 0.7377 (tmm) REVERT: C 621 MET cc_start: 0.6149 (pmm) cc_final: 0.5187 (ptp) REVERT: C 762 MET cc_start: 0.5823 (tmm) cc_final: 0.5511 (ptt) REVERT: D 402 ASP cc_start: 0.8248 (m-30) cc_final: 0.7726 (p0) REVERT: D 553 LYS cc_start: 0.7880 (tppt) cc_final: 0.7547 (tppt) REVERT: D 587 ASP cc_start: 0.7359 (t0) cc_final: 0.6625 (t0) REVERT: E 285 MET cc_start: 0.6857 (mmp) cc_final: 0.6369 (mmp) REVERT: E 288 MET cc_start: 0.7459 (mmm) cc_final: 0.7061 (mmm) REVERT: E 430 MET cc_start: 0.8235 (tpp) cc_final: 0.7857 (ttp) REVERT: E 614 LEU cc_start: 0.8818 (tt) cc_final: 0.8523 (pp) REVERT: E 784 MET cc_start: 0.7507 (mmp) cc_final: 0.7126 (mtp) REVERT: F 245 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9096 (tt) REVERT: F 359 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8248 (ttm110) REVERT: F 483 ASN cc_start: 0.7596 (p0) cc_final: 0.7140 (t0) REVERT: F 556 GLU cc_start: 0.8664 (mp0) cc_final: 0.8254 (mp0) REVERT: F 564 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7615 (pt0) REVERT: F 587 ASP cc_start: 0.8519 (t0) cc_final: 0.8165 (t0) REVERT: F 699 TYR cc_start: 0.9039 (t80) cc_final: 0.8787 (t80) REVERT: G 147 TYR cc_start: 0.8668 (m-80) cc_final: 0.8347 (m-10) REVERT: G 387 SER cc_start: 0.8632 (p) cc_final: 0.8347 (t) REVERT: H 288 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7675 (mt-10) REVERT: I 29 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8731 (ttpp) outliers start: 86 outliers final: 71 residues processed: 353 average time/residue: 0.2223 time to fit residues: 128.7427 Evaluate side-chains 344 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 28 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 0.0770 chunk 285 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN E 432 GLN F 295 ASN G 170 HIS G 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080770 restraints weight = 109826.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082609 restraints weight = 62752.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082718 restraints weight = 39166.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082976 restraints weight = 39914.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083004 restraints weight = 33490.111| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 34829 Z= 0.265 Angle : 0.707 10.909 47117 Z= 0.348 Chirality : 0.045 0.227 5306 Planarity : 0.004 0.050 6138 Dihedral : 9.475 147.652 4938 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 2.72 % Allowed : 13.78 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4274 helix: 1.49 (0.12), residues: 2045 sheet: -0.26 (0.22), residues: 564 loop : -0.41 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 369 TYR 0.035 0.002 TYR G 189 PHE 0.023 0.002 PHE G 381 TRP 0.015 0.002 TRP D 561 HIS 0.025 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00612 (34819) covalent geometry : angle 0.70588 (47111) hydrogen bonds : bond 0.03885 ( 1598) hydrogen bonds : angle 4.65288 ( 4506) metal coordination : bond 0.01818 ( 8) metal coordination : angle 3.92745 ( 6) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 274 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7546 (pmm) cc_final: 0.5946 (tpt) REVERT: A 56 MET cc_start: 0.7099 (ttp) cc_final: 0.6646 (tmm) REVERT: A 60 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7621 (pm20) REVERT: A 112 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 194 TRP cc_start: 0.1966 (p90) cc_final: 0.1091 (t60) REVERT: A 208 MET cc_start: 0.8684 (tmm) cc_final: 0.8386 (tmm) REVERT: A 398 MET cc_start: 0.8674 (mtp) cc_final: 0.8105 (mtm) REVERT: B 127 LEU cc_start: 0.8419 (mt) cc_final: 0.8069 (mm) REVERT: B 151 GLU cc_start: 0.7358 (mp0) cc_final: 0.5962 (tt0) REVERT: B 183 TYR cc_start: 0.7449 (p90) cc_final: 0.7067 (p90) REVERT: B 254 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7774 (p90) REVERT: B 315 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8323 (mm-30) REVERT: B 332 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: B 483 ASN cc_start: 0.8675 (t0) cc_final: 0.8288 (t0) REVERT: B 556 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8166 (mp0) REVERT: C 317 ASP cc_start: 0.7839 (p0) cc_final: 0.7600 (t0) REVERT: C 348 ARG cc_start: 0.8565 (mtt90) cc_final: 0.7635 (mmm160) REVERT: C 621 MET cc_start: 0.6188 (pmm) cc_final: 0.5352 (ptp) REVERT: C 762 MET cc_start: 0.5551 (tmm) cc_final: 0.5210 (ptt) REVERT: D 553 LYS cc_start: 0.7711 (tppt) cc_final: 0.7337 (tppt) REVERT: D 587 ASP cc_start: 0.7644 (t0) cc_final: 0.6935 (t0) REVERT: D 618 MET cc_start: 0.7634 (ttm) cc_final: 0.7344 (tmm) REVERT: E 285 MET cc_start: 0.7014 (mmp) cc_final: 0.6699 (mmp) REVERT: E 288 MET cc_start: 0.6864 (mmm) cc_final: 0.6522 (mmm) REVERT: E 430 MET cc_start: 0.8255 (tpp) cc_final: 0.7898 (ttp) REVERT: E 500 LYS cc_start: 0.6745 (mttt) cc_final: 0.6424 (ptpt) REVERT: E 614 LEU cc_start: 0.8856 (tt) cc_final: 0.8544 (pp) REVERT: E 784 MET cc_start: 0.7527 (mmp) cc_final: 0.7095 (mtp) REVERT: F 245 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9038 (tt) REVERT: F 359 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8313 (ttm110) REVERT: F 483 ASN cc_start: 0.7690 (p0) cc_final: 0.7091 (t0) REVERT: F 513 TYR cc_start: 0.8459 (m-80) cc_final: 0.7868 (m-80) REVERT: F 556 GLU cc_start: 0.8726 (mp0) cc_final: 0.8320 (mp0) REVERT: F 587 ASP cc_start: 0.8546 (t0) cc_final: 0.8201 (t0) REVERT: G 112 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7587 (ptm160) REVERT: G 190 ILE cc_start: 0.9187 (mm) cc_final: 0.8819 (pt) REVERT: G 387 SER cc_start: 0.8831 (p) cc_final: 0.8630 (p) REVERT: H 232 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8526 (p) REVERT: I 29 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8780 (ttpp) outliers start: 100 outliers final: 75 residues processed: 347 average time/residue: 0.2167 time to fit residues: 124.4396 Evaluate side-chains 337 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 302 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 287 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 404 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** 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 = 0.3953 r_free = 0.3953 target = 0.113848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082878 restraints weight = 110991.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083604 restraints weight = 65311.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083824 restraints weight = 44098.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084078 restraints weight = 43827.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084476 restraints weight = 36661.243| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34829 Z= 0.186 Angle : 0.652 11.852 47117 Z= 0.317 Chirality : 0.043 0.234 5306 Planarity : 0.004 0.050 6138 Dihedral : 9.335 147.737 4938 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 14.29 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4274 helix: 1.49 (0.12), residues: 2045 sheet: -0.28 (0.22), residues: 571 loop : -0.41 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 369 TYR 0.030 0.001 TYR G 189 PHE 0.016 0.001 PHE G 381 TRP 0.015 0.001 TRP D 561 HIS 0.019 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00429 (34819) covalent geometry : angle 0.64864 (47111) hydrogen bonds : bond 0.03496 ( 1598) hydrogen bonds : angle 4.52866 ( 4506) metal coordination : bond 0.01101 ( 8) metal coordination : angle 6.19214 ( 6) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7011 (ttp) cc_final: 0.6597 (tmm) REVERT: A 60 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7762 (pm20) REVERT: A 194 TRP cc_start: 0.1984 (p90) cc_final: 0.1090 (t60) REVERT: A 208 MET cc_start: 0.8670 (tmm) cc_final: 0.8365 (tmm) REVERT: A 398 MET cc_start: 0.8675 (mtp) cc_final: 0.8112 (mtm) REVERT: B 127 LEU cc_start: 0.8424 (mt) cc_final: 0.8086 (mm) REVERT: B 151 GLU cc_start: 0.7377 (mp0) cc_final: 0.5941 (tt0) REVERT: B 183 TYR cc_start: 0.7467 (p90) cc_final: 0.7085 (p90) REVERT: B 254 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7793 (p90) REVERT: B 315 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8281 (mm-30) REVERT: B 332 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.7007 (mtm-85) REVERT: B 483 ASN cc_start: 0.8703 (t0) cc_final: 0.8339 (t0) REVERT: C 317 ASP cc_start: 0.7819 (p0) cc_final: 0.7556 (t0) REVERT: C 348 ARG cc_start: 0.8540 (mtt90) cc_final: 0.7560 (mmm160) REVERT: C 359 ARG cc_start: 0.8552 (ptm160) cc_final: 0.8327 (ptm160) REVERT: C 370 PHE cc_start: 0.8635 (t80) cc_final: 0.8406 (t80) REVERT: C 621 MET cc_start: 0.6204 (pmm) cc_final: 0.5328 (ptp) REVERT: C 762 MET cc_start: 0.5563 (tmm) cc_final: 0.5212 (ptt) REVERT: D 553 LYS cc_start: 0.7723 (tppt) cc_final: 0.7377 (tppt) REVERT: D 587 ASP cc_start: 0.7642 (t0) cc_final: 0.6936 (t0) REVERT: D 618 MET cc_start: 0.7576 (ttm) cc_final: 0.7299 (tmm) REVERT: E 263 LEU cc_start: 0.8436 (tt) cc_final: 0.8040 (mm) REVERT: E 285 MET cc_start: 0.7085 (mmp) cc_final: 0.6788 (mmp) REVERT: E 288 MET cc_start: 0.6904 (mmm) cc_final: 0.6530 (mmm) REVERT: E 430 MET cc_start: 0.8249 (tpp) cc_final: 0.7842 (ttp) REVERT: E 614 LEU cc_start: 0.8863 (tt) cc_final: 0.8569 (pp) REVERT: E 784 MET cc_start: 0.7568 (mmp) cc_final: 0.7166 (mtp) REVERT: F 245 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9079 (tt) REVERT: F 359 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8324 (ttm110) REVERT: F 483 ASN cc_start: 0.7686 (p0) cc_final: 0.7077 (t0) REVERT: F 513 TYR cc_start: 0.8455 (m-80) cc_final: 0.7860 (m-80) REVERT: F 556 GLU cc_start: 0.8726 (mp0) cc_final: 0.8318 (mp0) REVERT: F 587 ASP cc_start: 0.8550 (t0) cc_final: 0.8237 (t0) REVERT: G 108 TYR cc_start: 0.6591 (m-80) cc_final: 0.6356 (m-80) REVERT: G 112 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7481 (ptm160) REVERT: G 190 ILE cc_start: 0.9153 (mm) cc_final: 0.8794 (pt) REVERT: H 232 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8556 (p) REVERT: H 288 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8032 (mt-10) outliers start: 84 outliers final: 66 residues processed: 325 average time/residue: 0.2186 time to fit residues: 117.0978 Evaluate side-chains 325 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 310 optimal weight: 0.0870 chunk 358 optimal weight: 0.3980 chunk 246 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 417 optimal weight: 0.3980 chunk 305 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 154 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.116421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085272 restraints weight = 110626.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086923 restraints weight = 60319.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086933 restraints weight = 37744.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087189 restraints weight = 39596.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087319 restraints weight = 32683.654| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34829 Z= 0.107 Angle : 0.626 11.672 47117 Z= 0.298 Chirality : 0.042 0.242 5306 Planarity : 0.004 0.043 6138 Dihedral : 8.926 146.304 4938 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 1.63 % Allowed : 14.84 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4274 helix: 1.70 (0.12), residues: 2023 sheet: -0.10 (0.22), residues: 567 loop : -0.25 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 369 TYR 0.028 0.001 TYR G 189 PHE 0.011 0.001 PHE B 162 TRP 0.014 0.001 TRP D 561 HIS 0.003 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00229 (34819) covalent geometry : angle 0.62405 (47111) hydrogen bonds : bond 0.02937 ( 1598) hydrogen bonds : angle 4.28042 ( 4506) metal coordination : bond 0.01207 ( 8) metal coordination : angle 4.38262 ( 6) Misc. bond : bond 0.00015 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7039 (ttp) cc_final: 0.6612 (tmm) REVERT: A 60 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7757 (pm20) REVERT: A 194 TRP cc_start: 0.1928 (p90) cc_final: 0.1117 (t60) REVERT: A 208 MET cc_start: 0.8681 (tmm) cc_final: 0.8375 (tmm) REVERT: A 254 TYR cc_start: 0.8787 (p90) cc_final: 0.8120 (p90) REVERT: A 398 MET cc_start: 0.8642 (mtp) cc_final: 0.8129 (mtm) REVERT: B 151 GLU cc_start: 0.7359 (mp0) cc_final: 0.5912 (tt0) REVERT: B 168 MET cc_start: 0.5292 (tpp) cc_final: 0.5004 (mtp) REVERT: B 183 TYR cc_start: 0.7462 (p90) cc_final: 0.7090 (p90) REVERT: B 315 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8218 (mm-30) REVERT: B 332 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6760 (mtm-85) REVERT: B 483 ASN cc_start: 0.8562 (t0) cc_final: 0.8021 (p0) REVERT: B 556 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8207 (mp0) REVERT: B 560 MET cc_start: 0.6134 (tpt) cc_final: 0.5907 (mtp) REVERT: C 348 ARG cc_start: 0.8616 (mtt90) cc_final: 0.7597 (mmm160) REVERT: C 621 MET cc_start: 0.6176 (pmm) cc_final: 0.5199 (ptp) REVERT: C 762 MET cc_start: 0.5687 (tmm) cc_final: 0.5321 (ptt) REVERT: D 293 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 553 LYS cc_start: 0.7734 (tppt) cc_final: 0.7380 (tppt) REVERT: D 587 ASP cc_start: 0.7472 (t0) cc_final: 0.6749 (t0) REVERT: D 618 MET cc_start: 0.7640 (ttm) cc_final: 0.7340 (tmm) REVERT: E 263 LEU cc_start: 0.8297 (tt) cc_final: 0.7891 (mm) REVERT: E 285 MET cc_start: 0.7067 (mmp) cc_final: 0.6774 (mmp) REVERT: E 288 MET cc_start: 0.6970 (mmm) cc_final: 0.6571 (mmm) REVERT: E 430 MET cc_start: 0.8224 (tpp) cc_final: 0.7782 (ttp) REVERT: E 614 LEU cc_start: 0.8824 (tt) cc_final: 0.8545 (pp) REVERT: E 762 MET cc_start: 0.8110 (ptt) cc_final: 0.7898 (ptt) REVERT: E 784 MET cc_start: 0.7567 (mmp) cc_final: 0.7168 (mtp) REVERT: F 245 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9096 (tt) REVERT: F 359 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8207 (ttm110) REVERT: F 483 ASN cc_start: 0.7603 (p0) cc_final: 0.7102 (t0) REVERT: F 513 TYR cc_start: 0.8480 (m-80) cc_final: 0.7865 (m-80) REVERT: F 556 GLU cc_start: 0.8690 (mp0) cc_final: 0.8291 (mp0) REVERT: F 564 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7582 (pt0) REVERT: F 587 ASP cc_start: 0.8484 (t0) cc_final: 0.8177 (t0) REVERT: F 621 MET cc_start: 0.8137 (ppp) cc_final: 0.7878 (ppp) REVERT: G 112 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7330 (ptm160) REVERT: G 147 TYR cc_start: 0.8731 (m-80) cc_final: 0.8434 (m-10) REVERT: H 232 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8421 (p) outliers start: 60 outliers final: 44 residues processed: 328 average time/residue: 0.2136 time to fit residues: 116.2906 Evaluate side-chains 316 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 716 HIS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 366 optimal weight: 4.9990 chunk 411 optimal weight: 0.6980 chunk 257 optimal weight: 0.6980 chunk 346 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 360 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.114624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084675 restraints weight = 109227.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.085320 restraints weight = 57859.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.085687 restraints weight = 40583.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085837 restraints weight = 40559.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086050 restraints weight = 33747.000| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34829 Z= 0.137 Angle : 0.632 11.281 47117 Z= 0.302 Chirality : 0.042 0.230 5306 Planarity : 0.004 0.045 6138 Dihedral : 8.762 145.550 4936 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 1.47 % Allowed : 15.43 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4274 helix: 1.67 (0.12), residues: 2035 sheet: -0.11 (0.22), residues: 569 loop : -0.27 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.037 0.001 TYR G 189 PHE 0.012 0.001 PHE G 260 TRP 0.014 0.001 TRP D 561 HIS 0.003 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00315 (34819) covalent geometry : angle 0.63034 (47111) hydrogen bonds : bond 0.03068 ( 1598) hydrogen bonds : angle 4.33217 ( 4506) metal coordination : bond 0.01019 ( 8) metal coordination : angle 4.36820 ( 6) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.06 seconds wall clock time: 107 minutes 31.20 seconds (6451.20 seconds total)