Starting phenix.real_space_refine on Sun Jun 29 17:30:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_27276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_27276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_27276.map" model { file = "/net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_27276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dau_27276/06_2025/8dau_27276.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.69, per 1000 atoms: 0.57 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: 10.30 Conformation dependent library (CDL) restraints added in 4.3 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: 4.38 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: 16.05 Time building geometry restraints manager: 10.69 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 786 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 33 through 786 or resid 901 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: 5.440 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: 1.510 Check model and map are aligned: 0.260 Set scattering table: 0.380 Process input model: 87.350 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.230 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: 0.030 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.730 ------------------------------------------------------------------------------- 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 : 9.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP G 489 HIS 0.004 0.001 HIS C 757 PHE 0.009 0.001 PHE C 275 TYR 0.020 0.001 TYR G 507 ARG 0.002 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.14428 ( 1598) hydrogen bonds : angle 5.33908 ( 4506) metal coordination : bond 0.06701 ( 8) metal coordination : angle 3.06690 ( 6) covalent geometry : bond 0.00349 (34819) covalent geometry : angle 0.92981 (47111) 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 : 4.028 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: 0.8634 (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: 0.5575 time to fit residues: 520.5759 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 : 4.054 ------------------------------------------------------------------------------- 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 362 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 336 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 389 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 113 HIS A 225 GLN A 394 HIS A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085858 restraints weight = 109766.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086435 restraints weight = 59074.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086727 restraints weight = 41721.634| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34829 Z= 0.172 Angle : 0.670 8.948 47117 Z= 0.328 Chirality : 0.045 0.242 5306 Planarity : 0.004 0.044 6138 Dihedral : 11.089 155.456 4957 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 1.85 % Allowed : 9.29 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.13), residues: 4274 helix: 1.90 (0.12), residues: 2019 sheet: 0.01 (0.23), residues: 545 loop : -0.09 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 486 HIS 0.029 0.001 HIS A 716 PHE 0.016 0.002 PHE G 260 TYR 0.022 0.001 TYR G 507 ARG 0.007 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1598) hydrogen bonds : angle 4.65374 ( 4506) metal coordination : bond 0.01336 ( 8) metal coordination : angle 3.39554 ( 6) covalent geometry : bond 0.00395 (34819) covalent geometry : angle 0.66913 (47111) Misc. bond : bond 0.00337 ( 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 419 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 4.033 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 60 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7094 (pm20) REVERT: A 194 TRP cc_start: 0.1757 (p90) cc_final: 0.0425 (t60) REVERT: A 229 MET cc_start: 0.8646 (mtt) cc_final: 0.8388 (mtt) REVERT: A 644 LEU cc_start: 0.8597 (mm) cc_final: 0.8204 (pp) REVERT: B 65 ASP cc_start: 0.4140 (OUTLIER) cc_final: 0.2553 (m-30) REVERT: B 86 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: B 183 TYR cc_start: 0.7069 (p90) cc_final: 0.6829 (p90) REVERT: B 315 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7966 (mm-30) REVERT: B 332 ARG cc_start: 0.6982 (mtm110) cc_final: 0.6405 (mpp80) REVERT: B 483 ASN cc_start: 0.8557 (t0) cc_final: 0.8093 (p0) REVERT: B 560 MET cc_start: 0.7303 (mtt) cc_final: 0.6951 (tpt) REVERT: B 588 GLU cc_start: 0.8402 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 778 GLU cc_start: 0.8473 (mp0) cc_final: 0.8248 (mm-30) REVERT: C 317 ASP cc_start: 0.7783 (p0) cc_final: 0.7506 (t0) REVERT: C 342 MET cc_start: 0.8675 (tpp) cc_final: 0.8195 (mmm) REVERT: C 570 ARG cc_start: 0.8215 (mmm160) cc_final: 0.6962 (tpp80) REVERT: C 649 LEU cc_start: 0.8993 (mm) cc_final: 0.8696 (tp) REVERT: D 314 ASP cc_start: 0.8265 (t0) cc_final: 0.8011 (t0) REVERT: D 331 GLU cc_start: 0.8400 (mp0) cc_final: 0.8048 (mp0) REVERT: D 402 ASP cc_start: 0.8175 (m-30) cc_final: 0.7747 (p0) REVERT: E 288 MET cc_start: 0.7007 (mmm) cc_final: 0.6485 (mmm) REVERT: E 430 MET cc_start: 0.8130 (tpp) cc_final: 0.7764 (ttp) REVERT: E 500 LYS cc_start: 0.7100 (mttt) cc_final: 0.6797 (ptpt) REVERT: E 614 LEU cc_start: 0.8808 (tt) cc_final: 0.8473 (pp) REVERT: E 784 MET cc_start: 0.7471 (mmp) cc_final: 0.7088 (mtp) REVERT: F 359 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8376 (ttm110) REVERT: F 483 ASN cc_start: 0.7664 (p0) cc_final: 0.7255 (t0) REVERT: F 556 GLU cc_start: 0.8764 (mp0) cc_final: 0.8279 (mp0) REVERT: F 587 ASP cc_start: 0.8428 (t0) cc_final: 0.8159 (t0) REVERT: F 588 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8637 (mt-10) REVERT: G 126 ASP cc_start: 0.8501 (p0) cc_final: 0.8288 (p0) REVERT: G 387 SER cc_start: 0.8547 (p) cc_final: 0.8288 (t) REVERT: G 422 MET cc_start: 0.8494 (mmm) cc_final: 0.8161 (mmm) REVERT: G 548 ILE cc_start: 0.9028 (pt) cc_final: 0.8734 (pt) REVERT: H 288 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7670 (mt-10) REVERT: I 29 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8717 (ttpp) outliers start: 68 outliers final: 32 residues processed: 397 average time/residue: 0.4803 time to fit residues: 306.2256 Evaluate side-chains 314 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 3.979 ------------------------------------------------------------------------------- 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 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 389 GLU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 LEU 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 229 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 422 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS B 193 HIS B 634 ASN E 280 ASN E 432 GLN F 337 GLN G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.109241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077908 restraints weight = 113424.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078738 restraints weight = 60206.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079134 restraints weight = 43005.801| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.168 34829 Z= 0.503 Angle : 0.937 12.858 47117 Z= 0.472 Chirality : 0.052 0.206 5306 Planarity : 0.006 0.070 6138 Dihedral : 11.141 147.542 4943 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 3.21 % Allowed : 11.63 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4274 helix: 0.74 (0.11), residues: 2051 sheet: -0.61 (0.22), residues: 559 loop : -0.72 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 486 HIS 0.013 0.002 HIS A 716 PHE 0.042 0.003 PHE G 381 TYR 0.031 0.003 TYR G 270 ARG 0.014 0.001 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 1598) hydrogen bonds : angle 5.50549 ( 4506) metal coordination : bond 0.03762 ( 8) metal coordination : angle 6.15990 ( 6) covalent geometry : bond 0.01148 (34819) covalent geometry : angle 0.93484 (47111) Misc. bond : bond 0.00049 ( 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 397 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 279 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6604 (ttp) cc_final: 0.6176 (tmm) REVERT: A 60 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7232 (pm20) REVERT: A 194 TRP cc_start: 0.1764 (p90) cc_final: 0.0564 (t60) REVERT: A 208 MET cc_start: 0.8746 (tmm) cc_final: 0.8373 (tmm) REVERT: B 127 LEU cc_start: 0.8409 (mt) cc_final: 0.8007 (mm) REVERT: B 183 TYR cc_start: 0.7227 (p90) cc_final: 0.6970 (p90) REVERT: B 315 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8241 (mm-30) REVERT: B 332 ARG cc_start: 0.7068 (mtm110) cc_final: 0.6455 (mpp80) REVERT: B 483 ASN cc_start: 0.8693 (t0) cc_final: 0.8395 (t0) REVERT: B 667 LEU cc_start: 0.7806 (mt) cc_final: 0.7559 (mt) REVERT: B 778 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: C 317 ASP cc_start: 0.7960 (p0) cc_final: 0.7666 (t70) REVERT: C 342 MET cc_start: 0.8878 (tpp) cc_final: 0.8192 (mmm) REVERT: C 444 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7143 (pt0) REVERT: C 570 ARG cc_start: 0.8285 (mmm160) cc_final: 0.6878 (tpp80) REVERT: C 571 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: C 618 MET cc_start: 0.7287 (tmm) cc_final: 0.7014 (tmm) REVERT: C 621 MET cc_start: 0.5891 (pmm) cc_final: 0.4937 (ptp) REVERT: C 699 TYR cc_start: 0.8631 (t80) cc_final: 0.8020 (m-80) REVERT: C 762 MET cc_start: 0.5578 (tmm) cc_final: 0.5332 (ptt) REVERT: D 314 ASP cc_start: 0.8462 (t0) cc_final: 0.8254 (t70) REVERT: D 331 GLU cc_start: 0.8346 (mp0) cc_final: 0.7893 (mp0) REVERT: E 285 MET cc_start: 0.7424 (mmp) cc_final: 0.6973 (mmp) REVERT: E 288 MET cc_start: 0.7259 (mmm) cc_final: 0.6833 (mmm) REVERT: E 430 MET cc_start: 0.8319 (tpp) cc_final: 0.7920 (ttp) REVERT: E 614 LEU cc_start: 0.8977 (tt) cc_final: 0.8622 (pp) REVERT: E 784 MET cc_start: 0.7558 (mmp) cc_final: 0.7127 (mtp) REVERT: F 254 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7537 (p90) REVERT: F 359 ARG cc_start: 0.8832 (tpp80) cc_final: 0.8527 (ttm110) REVERT: F 483 ASN cc_start: 0.7738 (p0) cc_final: 0.7191 (t0) REVERT: F 587 ASP cc_start: 0.8531 (t0) cc_final: 0.8200 (t0) REVERT: F 588 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8671 (mt-10) REVERT: G 133 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8390 (tptm) REVERT: G 422 MET cc_start: 0.8737 (mmm) cc_final: 0.8441 (mmm) REVERT: I 29 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8600 (tttt) outliers start: 118 outliers final: 76 residues processed: 377 average time/residue: 0.4727 time to fit residues: 291.5734 Evaluate side-chains 333 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 253 time to evaluate : 3.957 ------------------------------------------------------------------------------- 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 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 B residue 110 VAL Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 ARG 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 253 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 381 ILE 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 535 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 375 ARG 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 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 357 THR Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL 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 415 SER Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 578 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 134 GLU 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 207 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 363 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 414 optimal weight: 0.7980 chunk 269 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 358 ASN ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 612 ASN F 207 ASN F 337 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.083453 restraints weight = 108875.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084061 restraints weight = 57318.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084451 restraints weight = 40714.720| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34829 Z= 0.147 Angle : 0.636 9.050 47117 Z= 0.311 Chirality : 0.043 0.186 5306 Planarity : 0.004 0.058 6138 Dihedral : 10.547 140.773 4940 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 2.61 % Allowed : 13.15 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4274 helix: 1.32 (0.12), residues: 2036 sheet: -0.36 (0.22), residues: 574 loop : -0.46 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 252 HIS 0.004 0.001 HIS G 521 PHE 0.013 0.001 PHE B 162 TYR 0.035 0.001 TYR A 513 ARG 0.007 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1598) hydrogen bonds : angle 4.69139 ( 4506) metal coordination : bond 0.00703 ( 8) metal coordination : angle 2.56540 ( 6) covalent geometry : bond 0.00332 (34819) covalent geometry : angle 0.63489 (47111) Misc. bond : bond 0.00023 ( 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 386 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 290 time to evaluate : 3.770 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: 0.6676 (ttp) cc_final: 0.6207 (tmm) REVERT: A 60 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7342 (pm20) REVERT: A 194 TRP cc_start: 0.1770 (p90) cc_final: 0.0687 (t60) REVERT: A 208 MET cc_start: 0.8794 (tmm) cc_final: 0.8368 (tmm) REVERT: A 762 MET cc_start: 0.9011 (mmp) cc_final: 0.7197 (ptp) REVERT: B 86 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: B 151 GLU cc_start: 0.7314 (mp0) cc_final: 0.5665 (tm-30) REVERT: B 183 TYR cc_start: 0.7239 (p90) cc_final: 0.6927 (p90) REVERT: B 301 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 315 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: B 556 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8349 (mp0) REVERT: B 778 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: C 317 ASP cc_start: 0.7780 (p0) cc_final: 0.7500 (t0) REVERT: C 342 MET cc_start: 0.8700 (tpp) cc_final: 0.8102 (mmm) REVERT: C 437 MET cc_start: 0.8524 (tpp) cc_final: 0.8286 (tpp) REVERT: C 570 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7062 (tpp80) REVERT: C 571 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: C 618 MET cc_start: 0.7545 (tmm) cc_final: 0.7251 (tmm) REVERT: C 621 MET cc_start: 0.6050 (pmm) cc_final: 0.4985 (ptp) REVERT: C 762 MET cc_start: 0.5938 (tmm) cc_final: 0.5611 (ptt) REVERT: D 264 MET cc_start: 0.8047 (tmm) cc_final: 0.7817 (tmm) REVERT: D 331 GLU cc_start: 0.8391 (mp0) cc_final: 0.8049 (mp0) REVERT: D 402 ASP cc_start: 0.8352 (m-30) cc_final: 0.7788 (p0) REVERT: D 553 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7605 (pmtt) REVERT: E 263 LEU cc_start: 0.8595 (tt) cc_final: 0.8070 (mm) REVERT: E 430 MET cc_start: 0.8266 (tpp) cc_final: 0.7860 (ttp) REVERT: E 614 LEU cc_start: 0.8932 (tt) cc_final: 0.8608 (pp) REVERT: E 784 MET cc_start: 0.7499 (mmp) cc_final: 0.7120 (mtp) REVERT: F 264 MET cc_start: 0.8592 (tpt) cc_final: 0.8382 (tpp) REVERT: F 301 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: F 359 ARG cc_start: 0.8784 (tpp80) cc_final: 0.8392 (ttm110) REVERT: F 483 ASN cc_start: 0.7690 (p0) cc_final: 0.7241 (t0) REVERT: F 513 TYR cc_start: 0.8452 (m-80) cc_final: 0.7836 (m-10) REVERT: F 556 GLU cc_start: 0.8423 (mp0) cc_final: 0.8124 (mp0) REVERT: F 587 ASP cc_start: 0.8534 (t0) cc_final: 0.8216 (t0) REVERT: F 588 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8686 (mt-10) REVERT: G 112 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7589 (ptm160) REVERT: H 232 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8320 (p) outliers start: 96 outliers final: 53 residues processed: 363 average time/residue: 0.4651 time to fit residues: 276.3631 Evaluate side-chains 315 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 4.295 ------------------------------------------------------------------------------- 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 560 MET Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 633 THR 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 339 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 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 389 GLU Chi-restraints excluded: chain D residue 417 VAL 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 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 716 HIS Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 376 PHE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL 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 I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 2.9990 chunk 374 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 144 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN F 295 ASN ** G 205 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 = 0.3981 r_free = 0.3981 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084721 restraints weight = 111177.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085639 restraints weight = 56644.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086092 restraints weight = 39417.969| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34829 Z= 0.113 Angle : 0.615 10.889 47117 Z= 0.295 Chirality : 0.042 0.194 5306 Planarity : 0.004 0.048 6138 Dihedral : 9.965 135.091 4936 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 2.17 % Allowed : 13.86 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4274 helix: 1.61 (0.12), residues: 2029 sheet: -0.23 (0.22), residues: 575 loop : -0.35 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 252 HIS 0.003 0.001 HIS A 113 PHE 0.020 0.001 PHE D 628 TYR 0.027 0.001 TYR G 507 ARG 0.008 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1598) hydrogen bonds : angle 4.40867 ( 4506) metal coordination : bond 0.01022 ( 8) metal coordination : angle 5.32530 ( 6) covalent geometry : bond 0.00247 (34819) covalent geometry : angle 0.61209 (47111) Misc. bond : bond 0.00025 ( 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 367 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 4.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6779 (ttp) cc_final: 0.6311 (tmm) REVERT: A 60 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7517 (pm20) REVERT: A 161 HIS cc_start: 0.7578 (m-70) cc_final: 0.7371 (m-70) REVERT: A 194 TRP cc_start: 0.1850 (p90) cc_final: 0.0905 (t60) REVERT: A 208 MET cc_start: 0.8707 (tmm) cc_final: 0.8129 (tmm) REVERT: A 254 TYR cc_start: 0.8820 (p90) cc_final: 0.8542 (p90) REVERT: A 762 MET cc_start: 0.9064 (mmp) cc_final: 0.7332 (ptt) REVERT: B 60 GLU cc_start: 0.8359 (mp0) cc_final: 0.7830 (pp20) REVERT: B 86 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: B 183 TYR cc_start: 0.7444 (p90) cc_final: 0.7087 (p90) REVERT: B 301 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 315 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8216 (mm-30) REVERT: B 483 ASN cc_start: 0.8521 (t0) cc_final: 0.7963 (p0) REVERT: C 342 MET cc_start: 0.8578 (tpp) cc_final: 0.7936 (mmm) REVERT: C 437 MET cc_start: 0.8586 (tpp) cc_final: 0.8346 (tpp) REVERT: C 570 ARG cc_start: 0.8360 (mmm160) cc_final: 0.6970 (tpp80) REVERT: C 571 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: C 618 MET cc_start: 0.7480 (tmm) cc_final: 0.7239 (tmm) REVERT: C 621 MET cc_start: 0.6088 (pmm) cc_final: 0.5098 (ptp) REVERT: D 264 MET cc_start: 0.7932 (tmm) cc_final: 0.7722 (tmm) REVERT: D 402 ASP cc_start: 0.8322 (m-30) cc_final: 0.7757 (p0) REVERT: D 475 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.8155 (mmt-90) REVERT: D 587 ASP cc_start: 0.6953 (m-30) cc_final: 0.6710 (m-30) REVERT: E 263 LEU cc_start: 0.8494 (tt) cc_final: 0.8017 (mm) REVERT: E 285 MET cc_start: 0.7168 (mmp) cc_final: 0.6902 (mmp) REVERT: E 430 MET cc_start: 0.8257 (tpp) cc_final: 0.7845 (ttp) REVERT: E 614 LEU cc_start: 0.8897 (tt) cc_final: 0.8603 (pp) REVERT: E 784 MET cc_start: 0.7559 (mmp) cc_final: 0.7151 (mtp) REVERT: F 245 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9080 (tt) REVERT: F 264 MET cc_start: 0.8684 (tpt) cc_final: 0.8382 (tpt) REVERT: F 301 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: F 359 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8278 (ttm110) REVERT: F 483 ASN cc_start: 0.7666 (p0) cc_final: 0.7139 (t0) REVERT: F 513 TYR cc_start: 0.8477 (m-80) cc_final: 0.7832 (m-10) REVERT: F 556 GLU cc_start: 0.8404 (mp0) cc_final: 0.8127 (mp0) REVERT: F 587 ASP cc_start: 0.8540 (t0) cc_final: 0.8218 (t0) REVERT: F 588 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8713 (mt-10) REVERT: F 699 TYR cc_start: 0.9041 (t80) cc_final: 0.8795 (t80) REVERT: G 112 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7344 (ptm160) REVERT: G 147 TYR cc_start: 0.8843 (m-80) cc_final: 0.8509 (m-10) REVERT: H 232 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8202 (p) outliers start: 80 outliers final: 52 residues processed: 342 average time/residue: 0.4769 time to fit residues: 270.0650 Evaluate side-chains 324 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 3.726 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 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 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 633 THR 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 444 GLU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 262 THR 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 417 VAL 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 633 THR Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 301 GLU 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 G residue 148 CYS Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 336 ASP 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 G residue 477 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 161 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 312 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 280 ASN ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN F 337 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.109731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078236 restraints weight = 110373.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079826 restraints weight = 62998.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079909 restraints weight = 39629.496| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 34829 Z= 0.398 Angle : 0.837 12.273 47117 Z= 0.417 Chirality : 0.049 0.183 5306 Planarity : 0.005 0.059 6138 Dihedral : 10.193 133.332 4936 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 3.56 % Allowed : 13.99 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 4274 helix: 0.87 (0.11), residues: 2053 sheet: -0.61 (0.22), residues: 559 loop : -0.84 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 486 HIS 0.010 0.002 HIS G 139 PHE 0.032 0.003 PHE G 381 TYR 0.040 0.002 TYR G 189 ARG 0.007 0.001 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 1598) hydrogen bonds : angle 5.19328 ( 4506) metal coordination : bond 0.01676 ( 8) metal coordination : angle 6.48586 ( 6) covalent geometry : bond 0.00917 (34819) covalent geometry : angle 0.83409 (47111) Misc. bond : bond 0.00115 ( 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 395 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 264 time to evaluate : 3.729 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: 0.6792 (ttp) cc_final: 0.6334 (tmm) REVERT: A 60 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7619 (pm20) REVERT: A 161 HIS cc_start: 0.7709 (m-70) cc_final: 0.7495 (m-70) REVERT: A 194 TRP cc_start: 0.1577 (p90) cc_final: 0.0543 (t60) REVERT: A 208 MET cc_start: 0.8733 (tmm) cc_final: 0.8121 (tmm) REVERT: A 262 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7653 (m) REVERT: A 762 MET cc_start: 0.9015 (mmp) cc_final: 0.7265 (ptt) REVERT: B 60 GLU cc_start: 0.8407 (mp0) cc_final: 0.7873 (pm20) REVERT: B 151 GLU cc_start: 0.7358 (mp0) cc_final: 0.5694 (tm-30) REVERT: B 183 TYR cc_start: 0.7386 (p90) cc_final: 0.7022 (p90) REVERT: B 315 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: B 556 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8365 (mp0) REVERT: C 317 ASP cc_start: 0.7960 (p0) cc_final: 0.7669 (t0) REVERT: C 348 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8080 (mtt180) REVERT: C 359 ARG cc_start: 0.8506 (ptm160) cc_final: 0.7822 (ptm160) REVERT: C 416 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8419 (m-10) REVERT: C 437 MET cc_start: 0.8688 (tpp) cc_final: 0.8385 (tpp) REVERT: C 570 ARG cc_start: 0.8452 (mmm160) cc_final: 0.7127 (tpp80) REVERT: C 621 MET cc_start: 0.6141 (pmm) cc_final: 0.5317 (ptp) REVERT: C 762 MET cc_start: 0.5238 (tmm) cc_final: 0.4844 (ptt) REVERT: D 264 MET cc_start: 0.8396 (tmm) cc_final: 0.8038 (tmm) REVERT: D 475 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.8062 (mmt-90) REVERT: D 560 MET cc_start: 0.4822 (tmm) cc_final: 0.4577 (tmm) REVERT: E 285 MET cc_start: 0.7398 (mmp) cc_final: 0.6583 (mmp) REVERT: E 288 MET cc_start: 0.7329 (mmm) cc_final: 0.6752 (mmm) REVERT: E 430 MET cc_start: 0.8367 (tpp) cc_final: 0.7988 (ttp) REVERT: E 500 LYS cc_start: 0.6740 (mttt) cc_final: 0.6445 (mttt) REVERT: E 614 LEU cc_start: 0.8955 (tt) cc_final: 0.8555 (pp) REVERT: E 784 MET cc_start: 0.7473 (mmp) cc_final: 0.6997 (mtp) REVERT: F 245 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9056 (tt) REVERT: F 254 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7610 (p90) REVERT: F 301 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: F 359 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8248 (ttm110) REVERT: F 483 ASN cc_start: 0.7684 (p0) cc_final: 0.7101 (t0) REVERT: F 513 TYR cc_start: 0.8407 (m-80) cc_final: 0.7833 (m-80) REVERT: F 587 ASP cc_start: 0.8556 (t0) cc_final: 0.8170 (t0) REVERT: F 588 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8723 (mt-10) REVERT: F 621 MET cc_start: 0.8290 (ppp) cc_final: 0.7977 (ppp) REVERT: G 112 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7664 (ptm160) REVERT: G 422 MET cc_start: 0.8641 (mmm) cc_final: 0.7949 (mmm) REVERT: H 232 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8405 (p) outliers start: 131 outliers final: 90 residues processed: 369 average time/residue: 0.4432 time to fit residues: 270.0099 Evaluate side-chains 344 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 247 time to evaluate : 3.879 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 633 THR 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 381 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 262 THR 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 359 ARG Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 417 VAL 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 254 TYR 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 633 THR 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 254 TYR Chi-restraints excluded: chain F residue 301 GLU 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 536 LEU Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 387 SER 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 G residue 495 MET Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 238 MET 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 J residue 109 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 248 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 chunk 384 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 374 optimal weight: 0.7980 chunk 263 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN G 205 HIS J 168 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082145 restraints weight = 109330.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084571 restraints weight = 58306.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084385 restraints weight = 34488.991| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34829 Z= 0.125 Angle : 0.636 10.927 47117 Z= 0.309 Chirality : 0.043 0.266 5306 Planarity : 0.004 0.052 6138 Dihedral : 9.684 134.261 4936 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4274 helix: 1.33 (0.12), residues: 2036 sheet: -0.46 (0.21), residues: 577 loop : -0.58 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 561 HIS 0.003 0.001 HIS G 468 PHE 0.018 0.001 PHE B 62 TYR 0.029 0.001 TYR G 507 ARG 0.006 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1598) hydrogen bonds : angle 4.56833 ( 4506) metal coordination : bond 0.00913 ( 8) metal coordination : angle 3.59094 ( 6) covalent geometry : bond 0.00280 (34819) covalent geometry : angle 0.63459 (47111) Misc. bond : bond 0.00014 ( 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 360 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 269 time to evaluate : 3.979 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: 0.7099 (ttp) cc_final: 0.6745 (tmm) REVERT: A 60 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7659 (pm20) REVERT: A 161 HIS cc_start: 0.7661 (m-70) cc_final: 0.7446 (m-70) REVERT: A 194 TRP cc_start: 0.1811 (p90) cc_final: 0.0986 (t60) REVERT: A 208 MET cc_start: 0.8702 (tmm) cc_final: 0.8055 (tmm) REVERT: A 398 MET cc_start: 0.8681 (mtp) cc_final: 0.8096 (mtm) REVERT: A 762 MET cc_start: 0.9022 (mmp) cc_final: 0.7372 (ptt) REVERT: B 151 GLU cc_start: 0.7418 (mp0) cc_final: 0.5831 (tm-30) REVERT: B 183 TYR cc_start: 0.7404 (p90) cc_final: 0.7044 (p90) REVERT: B 301 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 315 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8275 (mm-30) REVERT: B 556 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8175 (mp0) REVERT: C 342 MET cc_start: 0.8610 (tpp) cc_final: 0.8108 (mpp) REVERT: C 348 ARG cc_start: 0.8501 (mtt90) cc_final: 0.7554 (mmm160) REVERT: C 359 ARG cc_start: 0.8535 (ptm160) cc_final: 0.7946 (ptm160) REVERT: C 437 MET cc_start: 0.8714 (tpp) cc_final: 0.8495 (tpp) REVERT: C 570 ARG cc_start: 0.8358 (mmm160) cc_final: 0.6953 (tpp80) REVERT: C 621 MET cc_start: 0.6186 (pmm) cc_final: 0.5515 (ptp) REVERT: C 762 MET cc_start: 0.5666 (tmm) cc_final: 0.5284 (ptt) REVERT: D 264 MET cc_start: 0.8109 (tmm) cc_final: 0.7688 (tmm) REVERT: D 475 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.8146 (mmt-90) REVERT: E 263 LEU cc_start: 0.8341 (tt) cc_final: 0.7903 (mm) REVERT: E 430 MET cc_start: 0.8268 (tpp) cc_final: 0.7901 (ttp) REVERT: E 614 LEU cc_start: 0.8860 (tt) cc_final: 0.8555 (pp) REVERT: E 784 MET cc_start: 0.7523 (mmp) cc_final: 0.7096 (mtp) REVERT: F 245 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9062 (tt) REVERT: F 301 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: F 359 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8261 (ttm110) REVERT: F 483 ASN cc_start: 0.7665 (p0) cc_final: 0.7094 (t0) REVERT: F 513 TYR cc_start: 0.8441 (m-80) cc_final: 0.7832 (m-80) REVERT: F 556 GLU cc_start: 0.8425 (mp0) cc_final: 0.8095 (mp0) REVERT: F 577 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7605 (mtm-85) REVERT: F 587 ASP cc_start: 0.8567 (t0) cc_final: 0.8227 (t0) REVERT: F 588 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8726 (mt-10) REVERT: F 621 MET cc_start: 0.8132 (ppp) cc_final: 0.7870 (ppp) REVERT: F 699 TYR cc_start: 0.9010 (t80) cc_final: 0.8802 (t80) REVERT: G 112 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7477 (ptm160) REVERT: G 190 ILE cc_start: 0.9130 (mm) cc_final: 0.8804 (pt) REVERT: G 422 MET cc_start: 0.8556 (mmm) cc_final: 0.8241 (mmm) REVERT: H 288 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8086 (mt-10) outliers start: 91 outliers final: 65 residues processed: 336 average time/residue: 0.4878 time to fit residues: 273.7686 Evaluate side-chains 322 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 633 THR 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 541 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 253 MET 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 417 VAL 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 633 THR Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain F residue 364 ASP 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 225 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 376 PHE 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 238 MET 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 J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 291 optimal weight: 0.0770 chunk 147 optimal weight: 0.3980 chunk 354 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN E 638 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.114295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083584 restraints weight = 111296.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083968 restraints weight = 63652.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084319 restraints weight = 45883.848| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34829 Z= 0.134 Angle : 0.628 10.881 47117 Z= 0.303 Chirality : 0.043 0.253 5306 Planarity : 0.004 0.050 6138 Dihedral : 9.350 138.865 4936 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 2.12 % Allowed : 15.92 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4274 helix: 1.44 (0.12), residues: 2036 sheet: -0.37 (0.22), residues: 563 loop : -0.53 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 561 HIS 0.028 0.001 HIS G 205 PHE 0.015 0.001 PHE B 62 TYR 0.033 0.001 TYR G 189 ARG 0.005 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 1598) hydrogen bonds : angle 4.47506 ( 4506) metal coordination : bond 0.01121 ( 8) metal coordination : angle 3.59090 ( 6) covalent geometry : bond 0.00306 (34819) covalent geometry : angle 0.62644 (47111) Misc. bond : bond 0.00026 ( 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 345 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 267 time to evaluate : 3.967 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: 0.7030 (ttp) cc_final: 0.6612 (tmm) REVERT: A 60 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7707 (pm20) REVERT: A 161 HIS cc_start: 0.7656 (m-70) cc_final: 0.7453 (m-70) REVERT: A 194 TRP cc_start: 0.1834 (p90) cc_final: 0.0968 (t60) REVERT: A 208 MET cc_start: 0.8722 (tmm) cc_final: 0.8428 (tmm) REVERT: A 398 MET cc_start: 0.8699 (mtp) cc_final: 0.8134 (mtm) REVERT: A 762 MET cc_start: 0.9056 (mmp) cc_final: 0.7433 (ptt) REVERT: B 183 TYR cc_start: 0.7442 (p90) cc_final: 0.7079 (p90) REVERT: B 301 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8006 (tm-30) REVERT: B 315 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8259 (mm-30) REVERT: C 342 MET cc_start: 0.8666 (tpp) cc_final: 0.8096 (mpp) REVERT: C 348 ARG cc_start: 0.8481 (mtt90) cc_final: 0.7558 (mmm160) REVERT: C 570 ARG cc_start: 0.8347 (mmm160) cc_final: 0.6880 (tpp80) REVERT: C 621 MET cc_start: 0.6235 (pmm) cc_final: 0.5335 (ptp) REVERT: C 762 MET cc_start: 0.5505 (tmm) cc_final: 0.5069 (ptt) REVERT: D 264 MET cc_start: 0.8135 (tmm) cc_final: 0.7816 (tmm) REVERT: D 475 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8163 (mmt-90) REVERT: E 263 LEU cc_start: 0.8331 (tt) cc_final: 0.7888 (mm) REVERT: E 285 MET cc_start: 0.7211 (mmp) cc_final: 0.6583 (mmp) REVERT: E 288 MET cc_start: 0.7162 (mmm) cc_final: 0.6625 (mmm) REVERT: E 430 MET cc_start: 0.8298 (tpp) cc_final: 0.7900 (ttp) REVERT: E 614 LEU cc_start: 0.8856 (tt) cc_final: 0.8554 (pp) REVERT: E 784 MET cc_start: 0.7544 (mmp) cc_final: 0.7107 (mtp) REVERT: F 245 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9030 (tt) REVERT: F 301 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: F 359 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8152 (ttm110) REVERT: F 483 ASN cc_start: 0.7654 (p0) cc_final: 0.7088 (t0) REVERT: F 513 TYR cc_start: 0.8466 (m-80) cc_final: 0.7850 (m-80) REVERT: F 556 GLU cc_start: 0.8427 (mp0) cc_final: 0.8109 (mp0) REVERT: F 577 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7561 (mtm-85) REVERT: F 587 ASP cc_start: 0.8574 (t0) cc_final: 0.8230 (t0) REVERT: F 588 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8737 (mt-10) REVERT: F 699 TYR cc_start: 0.9052 (t80) cc_final: 0.8827 (t80) REVERT: F 703 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8455 (tpp-160) REVERT: G 112 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7389 (ptm160) REVERT: G 190 ILE cc_start: 0.9087 (mm) cc_final: 0.8766 (pt) REVERT: H 288 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7916 (mt-10) outliers start: 78 outliers final: 59 residues processed: 327 average time/residue: 0.4665 time to fit residues: 249.1650 Evaluate side-chains 318 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 633 THR 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 444 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 229 MET 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 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 253 MET Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 633 THR 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 301 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 703 ARG Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 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 238 MET 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 J residue 166 THR Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 85 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 285 optimal weight: 0.0270 chunk 393 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 255 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS D 280 ASN G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.115233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085872 restraints weight = 108707.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086194 restraints weight = 58578.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086699 restraints weight = 42082.067| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34829 Z= 0.119 Angle : 0.628 11.067 47117 Z= 0.300 Chirality : 0.042 0.251 5306 Planarity : 0.004 0.054 6138 Dihedral : 9.041 141.412 4936 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 1.98 % Allowed : 16.30 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4274 helix: 1.54 (0.12), residues: 2032 sheet: -0.29 (0.22), residues: 561 loop : -0.44 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 561 HIS 0.004 0.001 HIS G 205 PHE 0.014 0.001 PHE B 62 TYR 0.026 0.001 TYR G 507 ARG 0.016 0.000 ARG G 203 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 1598) hydrogen bonds : angle 4.35518 ( 4506) metal coordination : bond 0.01267 ( 8) metal coordination : angle 3.67889 ( 6) covalent geometry : bond 0.00265 (34819) covalent geometry : angle 0.62645 (47111) Misc. bond : bond 0.00025 ( 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 356 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 283 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7697 (pmm) cc_final: 0.6130 (tpt) REVERT: A 56 MET cc_start: 0.7069 (ttp) cc_final: 0.6656 (tmm) REVERT: A 60 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7646 (pm20) REVERT: A 194 TRP cc_start: 0.1760 (p90) cc_final: 0.1104 (t60) REVERT: A 208 MET cc_start: 0.8732 (tmm) cc_final: 0.8433 (tmm) REVERT: A 342 MET cc_start: 0.8863 (mtp) cc_final: 0.8608 (mtp) REVERT: A 398 MET cc_start: 0.8638 (mtp) cc_final: 0.8119 (mtm) REVERT: A 762 MET cc_start: 0.9070 (mmp) cc_final: 0.7437 (ptt) REVERT: B 151 GLU cc_start: 0.7244 (mp0) cc_final: 0.6016 (tt0) REVERT: B 168 MET cc_start: 0.5586 (tpp) cc_final: 0.5274 (tpp) REVERT: B 183 TYR cc_start: 0.7411 (p90) cc_final: 0.7049 (p90) REVERT: B 301 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 315 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8263 (mm-30) REVERT: B 332 ARG cc_start: 0.6983 (ttm170) cc_final: 0.6585 (mpt-90) REVERT: B 483 ASN cc_start: 0.8505 (t0) cc_final: 0.8013 (p0) REVERT: C 342 MET cc_start: 0.8627 (tpp) cc_final: 0.8122 (mpp) REVERT: C 348 ARG cc_start: 0.8516 (mtt90) cc_final: 0.7525 (mmm160) REVERT: C 370 PHE cc_start: 0.8580 (t80) cc_final: 0.8278 (t80) REVERT: C 416 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: C 570 ARG cc_start: 0.8416 (mmm160) cc_final: 0.6902 (tpp80) REVERT: C 621 MET cc_start: 0.6380 (pmm) cc_final: 0.5422 (ptp) REVERT: C 762 MET cc_start: 0.5496 (tmm) cc_final: 0.5092 (ptt) REVERT: D 475 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8145 (mmt-90) REVERT: D 618 MET cc_start: 0.8105 (ttm) cc_final: 0.7847 (ptm) REVERT: E 263 LEU cc_start: 0.8306 (tt) cc_final: 0.7856 (mm) REVERT: E 285 MET cc_start: 0.7053 (mmp) cc_final: 0.6837 (mmp) REVERT: E 398 MET cc_start: 0.6511 (mtm) cc_final: 0.6178 (mtm) REVERT: E 430 MET cc_start: 0.8289 (tpp) cc_final: 0.7909 (ttp) REVERT: E 614 LEU cc_start: 0.8891 (tt) cc_final: 0.8554 (pp) REVERT: E 762 MET cc_start: 0.8123 (ptt) cc_final: 0.7901 (ptt) REVERT: E 784 MET cc_start: 0.7449 (mmp) cc_final: 0.7061 (mtp) REVERT: F 245 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9126 (tt) REVERT: F 301 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: F 359 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8171 (ttm110) REVERT: F 483 ASN cc_start: 0.7616 (p0) cc_final: 0.7095 (t0) REVERT: F 513 TYR cc_start: 0.8435 (m-80) cc_final: 0.7856 (m-80) REVERT: F 556 GLU cc_start: 0.8423 (mp0) cc_final: 0.8083 (mp0) REVERT: F 587 ASP cc_start: 0.8551 (t0) cc_final: 0.8198 (t0) REVERT: F 588 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8740 (mt-10) REVERT: F 618 MET cc_start: 0.8871 (tpt) cc_final: 0.8588 (tpt) REVERT: F 699 TYR cc_start: 0.9022 (t80) cc_final: 0.8805 (t80) REVERT: G 112 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7353 (ptm160) REVERT: H 288 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7745 (mt-10) outliers start: 73 outliers final: 58 residues processed: 337 average time/residue: 0.4696 time to fit residues: 258.0772 Evaluate side-chains 324 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 633 THR 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 416 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain D residue 229 MET 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 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 633 THR 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 301 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 703 ARG Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 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 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 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 320 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 408 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 309 optimal weight: 0.8980 chunk 395 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS D 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.113494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082880 restraints weight = 109120.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084171 restraints weight = 60743.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084597 restraints weight = 38365.446| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34829 Z= 0.158 Angle : 0.648 14.729 47117 Z= 0.311 Chirality : 0.043 0.240 5306 Planarity : 0.004 0.048 6138 Dihedral : 8.945 141.653 4936 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 1.90 % Allowed : 16.52 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 4274 helix: 1.53 (0.12), residues: 2032 sheet: -0.31 (0.22), residues: 558 loop : -0.47 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 561 HIS 0.004 0.001 HIS G 139 PHE 0.014 0.001 PHE B 62 TYR 0.039 0.001 TYR G 189 ARG 0.007 0.000 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 1598) hydrogen bonds : angle 4.44008 ( 4506) metal coordination : bond 0.00955 ( 8) metal coordination : angle 3.50370 ( 6) covalent geometry : bond 0.00365 (34819) covalent geometry : angle 0.64705 (47111) Misc. bond : bond 0.00033 ( 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 333 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 4.302 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: 0.7061 (ttp) cc_final: 0.6641 (tmm) REVERT: A 60 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7680 (pm20) REVERT: A 194 TRP cc_start: 0.1870 (p90) cc_final: 0.1171 (t60) REVERT: A 208 MET cc_start: 0.8698 (tmm) cc_final: 0.8400 (tmm) REVERT: A 398 MET cc_start: 0.8694 (mtp) cc_final: 0.8181 (mtm) REVERT: A 762 MET cc_start: 0.9037 (mmp) cc_final: 0.7440 (ptt) REVERT: B 151 GLU cc_start: 0.7291 (mp0) cc_final: 0.5898 (tt0) REVERT: B 183 TYR cc_start: 0.7432 (p90) cc_final: 0.7066 (p90) REVERT: B 263 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8435 (tt) REVERT: B 301 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 315 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8290 (mm-30) REVERT: B 332 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6817 (mtt90) REVERT: B 556 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8310 (mp0) REVERT: C 342 MET cc_start: 0.8743 (tpp) cc_final: 0.8190 (mpp) REVERT: C 348 ARG cc_start: 0.8495 (mtt90) cc_final: 0.7530 (mmm160) REVERT: C 370 PHE cc_start: 0.8623 (t80) cc_final: 0.8319 (t80) REVERT: C 416 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: C 570 ARG cc_start: 0.8365 (mmm160) cc_final: 0.6881 (tpp80) REVERT: C 621 MET cc_start: 0.6364 (pmm) cc_final: 0.5573 (ptp) REVERT: C 762 MET cc_start: 0.5492 (tmm) cc_final: 0.5080 (ptt) REVERT: D 475 ARG cc_start: 0.8373 (mmt-90) cc_final: 0.8141 (mmt-90) REVERT: E 263 LEU cc_start: 0.8390 (tt) cc_final: 0.7926 (mm) REVERT: E 285 MET cc_start: 0.7192 (mmp) cc_final: 0.6503 (mmp) REVERT: E 288 MET cc_start: 0.7282 (mmm) cc_final: 0.6787 (mmm) REVERT: E 430 MET cc_start: 0.8291 (tpp) cc_final: 0.7906 (ttp) REVERT: E 614 LEU cc_start: 0.8821 (tt) cc_final: 0.8535 (pp) REVERT: E 784 MET cc_start: 0.7493 (mmp) cc_final: 0.7067 (mtp) REVERT: F 245 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9071 (tt) REVERT: F 301 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: F 359 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8276 (ttm110) REVERT: F 483 ASN cc_start: 0.7633 (p0) cc_final: 0.7085 (t0) REVERT: F 513 TYR cc_start: 0.8445 (m-80) cc_final: 0.7854 (m-80) REVERT: F 556 GLU cc_start: 0.8418 (mp0) cc_final: 0.8100 (mp0) REVERT: F 587 ASP cc_start: 0.8578 (t0) cc_final: 0.8223 (t0) REVERT: F 588 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8720 (mt-10) REVERT: F 699 TYR cc_start: 0.9062 (t80) cc_final: 0.8838 (t80) REVERT: G 112 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7269 (ptm160) REVERT: G 205 HIS cc_start: 0.8256 (p-80) cc_final: 0.8021 (p90) REVERT: H 288 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7827 (mt-10) outliers start: 70 outliers final: 58 residues processed: 319 average time/residue: 0.4646 time to fit residues: 244.9897 Evaluate side-chains 321 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 633 THR 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 416 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 574 ASP 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 389 GLU Chi-restraints excluded: chain D residue 417 VAL 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 482 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 633 THR 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 301 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 703 ARG Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 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 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 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 426 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS F 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081881 restraints weight = 110547.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083222 restraints weight = 60186.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083685 restraints weight = 39384.254| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34829 Z= 0.187 Angle : 0.677 12.931 47117 Z= 0.327 Chirality : 0.044 0.294 5306 Planarity : 0.004 0.084 6138 Dihedral : 8.974 141.066 4936 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 1.93 % Allowed : 16.63 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4274 helix: 1.47 (0.12), residues: 2032 sheet: -0.43 (0.22), residues: 574 loop : -0.48 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 561 HIS 0.005 0.001 HIS G 139 PHE 0.018 0.001 PHE G 381 TYR 0.036 0.001 TYR G 189 ARG 0.015 0.000 ARG G 203 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 1598) hydrogen bonds : angle 4.53883 ( 4506) metal coordination : bond 0.00885 ( 8) metal coordination : angle 3.54253 ( 6) covalent geometry : bond 0.00432 (34819) covalent geometry : angle 0.67541 (47111) Misc. bond : bond 0.00039 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11405.58 seconds wall clock time: 198 minutes 0.51 seconds (11880.51 seconds total)