Starting phenix.real_space_refine on Sun Jun 29 14:53:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.map" model { file = "/net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dav_27277/06_2025/8dav_27277.cif" } resolution = 3.5 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= 1.081 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 2 residue(s): 0.12s 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 45.745 49.270 92.930 1.00 77.95 S ATOM 28425 SG CYS G 145 49.375 50.017 93.042 1.00 58.37 S ATOM 28452 SG CYS G 148 47.278 50.134 96.007 1.00 56.03 S ATOM 28922 SG CYS G 204 73.882 91.093 114.110 1.00 86.29 S ATOM 29020 SG CYS G 216 74.129 91.033 110.344 1.00 61.09 S ATOM 29041 SG CYS G 219 71.340 92.806 111.935 1.00 66.42 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU K 273 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU K 273 " occ=0.00 residue: pdb=" N ARG K 274 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG K 274 " occ=0.00 residue: pdb=" N GLY K 275 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 275 " occ=0.00 residue: pdb=" N GLY K 276 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 276 " occ=0.00 Time building chain proxies: 19.00, per 1000 atoms: 0.55 Number of scatterers: 34248 At special positions: 0 Unit cell: (150.024, 169.176, 189.392, 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " 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: 209 helices and 25 sheets defined 53.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.630A pdb=" N MET A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.629A pdb=" N ARG A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.776A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.172A 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: 4.034A 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: 4.149A 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: 3.574A 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: 3.659A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.517A pdb=" N ARG A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.836A 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: 3.523A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 removed outlier: 4.441A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.522A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.506A 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: 4.464A 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: 4.176A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.627A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.510A 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: 3.707A 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: 3.673A 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 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.039A pdb=" N GLU B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 4.478A pdb=" N VAL B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.717A 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 231 Processing helix chain 'B' and resid 236 through 244 removed outlier: 4.196A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.574A pdb=" N MET B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 315 through 319 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 437 Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.572A pdb=" N LEU B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.332A 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: 4.153A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.540A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 588 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: 3.986A pdb=" N ARG B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 671 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: 3.859A 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: 3.629A 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 237 through 244 removed outlier: 3.631A 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: 3.851A pdb=" N ILE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.941A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.859A 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: 3.521A 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 448 through 454 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 492 through 503 removed outlier: 4.362A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 509 Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.938A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 553 through 563 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: 4.180A pdb=" N LEU C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.831A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 786 removed outlier: 3.816A 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: 4.247A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 241 " --> pdb=" O PRO D 237 " (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: 4.068A 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 437 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: 3.623A 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: 3.516A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.740A 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 Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.428A 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 592 Processing helix chain 'D' and resid 608 through 620 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: 4.032A pdb=" N LEU D 697 " --> pdb=" O SER D 693 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 removed outlier: 4.216A 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: 4.393A 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: 3.955A pdb=" N VAL E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 removed outlier: 3.674A pdb=" N SER E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 345 removed outlier: 3.934A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.560A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 369 " --> pdb=" O ALA E 366 " (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 448 through 455 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: 4.132A 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 546 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 removed outlier: 3.567A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 620 Processing helix chain 'E' and resid 640 through 645 removed outlier: 3.902A 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 688 removed outlier: 3.867A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 718 Processing helix chain 'E' and resid 754 through 764 removed outlier: 4.163A 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 206 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 3.983A 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: 4.460A 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 288 through 306 removed outlier: 4.451A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 3.900A pdb=" N ILE F 319 " --> pdb=" O GLU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.520A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 369 removed outlier: 3.954A 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: 3.873A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.770A 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: 3.677A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.519A 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 589 through 593 removed outlier: 3.645A pdb=" N ILE F 592 " --> pdb=" O LEU F 589 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 593 " --> pdb=" O ASP F 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 589 through 593' Processing helix chain 'F' and resid 608 through 621 Processing helix chain 'F' and resid 635 through 639 Processing helix chain 'F' and resid 640 through 645 removed outlier: 3.572A pdb=" N ARG F 645 " --> pdb=" O ALA F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 671 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 Processing helix chain 'F' and resid 770 through 786 removed outlier: 3.529A pdb=" N LEU F 774 " --> pdb=" O SER F 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 Processing helix chain 'G' and resid 155 through 163 removed outlier: 3.502A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.903A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 174 " --> pdb=" O HIS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 removed outlier: 3.567A pdb=" N GLY G 214 " --> pdb=" O TRP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 256 removed outlier: 4.495A pdb=" N ILE G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.643A pdb=" N VAL G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 Processing helix chain 'G' and resid 402 through 409 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: 3.710A 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 565 removed outlier: 4.233A pdb=" N SER G 559 " --> pdb=" O GLU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.537A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 234 removed outlier: 3.729A pdb=" N LEU H 233 " --> pdb=" O PRO H 230 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY H 234 " --> pdb=" O SER H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 254 removed outlier: 3.805A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'I' and resid 22 through 31 removed outlier: 3.532A pdb=" N VAL I 26 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 155 through 160 Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.995A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 241 Processing helix chain 'K' and resid 255 through 260 removed outlier: 4.043A pdb=" N TYR K 259 " --> pdb=" O THR K 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.021A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA A 187 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ARG A 123 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N ASP A 189 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N SER A 125 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ILE A 191 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N LEU A 127 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N HIS A 193 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 280 removed outlier: 6.768A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 357 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 548 through 552 removed outlier: 3.637A pdb=" N THR A 633 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 removed outlier: 7.089A pdb=" N LYS B 119 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.204A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.398A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY B 250 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL B 377 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 548 through 552 removed outlier: 3.572A pdb=" N VAL B 583 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.046A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 357 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 524 through 527 Processing sheet with id=AB3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AB4, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.364A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 357 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 548 through 553 removed outlier: 6.327A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 279 removed outlier: 3.895A pdb=" N ALA E 356 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E 253 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 357 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY E 250 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 548 through 552 removed outlier: 3.941A pdb=" N VAL E 583 " --> pdb=" O ASN E 548 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 275 through 278 removed outlier: 6.982A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 309 " --> pdb=" O ASN F 350 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 548 through 552 removed outlier: 3.615A pdb=" N VAL F 524 " --> pdb=" O VAL F 629 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 236 through 239 removed outlier: 3.657A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 290 through 291 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 Processing sheet with id=AC5, first strand: chain 'G' and resid 470 through 471 Processing sheet with id=AC6, first strand: chain 'J' and resid 112 through 116 Processing sheet with id=AC7, first strand: chain 'K' and resid 212 through 215 removed outlier: 6.337A pdb=" N PHE K 204 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU K 269 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS K 206 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE K 245 " --> pdb=" O LYS K 248 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4524 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: 12.29 Time building geometry restraints manager: 10.16 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: 11585 1.34 - 1.46: 5476 1.46 - 1.58: 17425 1.58 - 1.69: 45 1.69 - 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 3.06e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 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 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 46837 5.72 - 11.44: 234 11.44 - 17.17: 33 17.17 - 22.89: 6 22.89 - 28.61: 1 Bond angle restraints: 47111 Sorted by residual: angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 120.54 140.12 -19.58 1.35e+00 5.49e-01 2.10e+02 angle pdb=" C MET B 229 " pdb=" N VAL B 230 " pdb=" CA VAL B 230 " ideal model delta sigma weight residual 120.88 137.37 -16.49 1.22e+00 6.72e-01 1.83e+02 angle pdb=" C ASP B 314 " pdb=" N GLU B 315 " pdb=" CA GLU B 315 " ideal model delta sigma weight residual 122.82 140.42 -17.60 1.42e+00 4.96e-01 1.54e+02 angle pdb=" C ARG B 672 " pdb=" N LYS B 673 " pdb=" CA LYS B 673 " ideal model delta sigma weight residual 120.29 137.76 -17.47 1.42e+00 4.96e-01 1.51e+02 angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 150.41 -28.61 2.44e+00 1.68e-01 1.37e+02 ... (remaining 47106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 21262 33.10 - 66.21: 243 66.21 - 99.31: 22 99.31 - 132.41: 16 132.41 - 165.52: 5 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 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.36e+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 -102.94 -165.52 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -122.76 -145.69 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 21545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 5176 0.348 - 0.695: 63 0.695 - 1.043: 0 1.043 - 1.391: 13 1.391 - 1.738: 54 Chirality restraints: 5306 Sorted by residual: chirality pdb=" CG LEU J 115 " pdb=" CB LEU J 115 " pdb=" CD1 LEU J 115 " pdb=" CD2 LEU J 115 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.55e+01 chirality pdb=" CG LEU F 558 " pdb=" CB LEU F 558 " pdb=" CD1 LEU F 558 " pdb=" CD2 LEU F 558 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CG LEU E 234 " pdb=" CB LEU E 234 " pdb=" CD1 LEU E 234 " pdb=" CD2 LEU E 234 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 ... (remaining 5303 not shown) Planarity restraints: 6138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C GLU B 329 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU B 329 " 0.013 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 LYS G 506 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS G 506 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR G 507 " 0.010 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 1.55e-02 2.42e+00 pdb=" C SER F 294 " -0.027 2.00e-02 2.50e+03 pdb=" O SER F 294 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN F 295 " 0.009 2.00e-02 2.50e+03 ... (remaining 6135 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 372 2.53 - 3.12: 29065 3.12 - 3.71: 52584 3.71 - 4.31: 69264 4.31 - 4.90: 118291 Nonbonded interactions: 269576 Sorted by model distance: nonbonded pdb=" OG SER D 559 " pdb=" O GLU D 564 " model vdw 1.934 3.040 nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.941 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" O CYS B 115 " model vdw 1.991 3.040 nonbonded pdb=" OG SER B 286 " pdb=" OE1 GLU B 291 " model vdw 1.992 3.040 nonbonded pdb=" OG1 THR D 262 " pdb=" O2G ATP D 901 " model vdw 2.002 3.040 ... (remaining 269571 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 1.430 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 79.370 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.901 34830 Z= 0.520 Angle : 0.956 28.610 47117 Z= 0.487 Chirality : 0.188 1.738 5306 Planarity : 0.003 0.032 6138 Dihedral : 11.635 165.517 13424 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 0.79 % Allowed : 4.13 % Favored : 95.08 % 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: 1.53 (0.14), residues: 4274 helix: 2.26 (0.12), residues: 1991 sheet: -0.24 (0.23), residues: 551 loop : 0.04 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 252 HIS 0.005 0.001 HIS G 236 PHE 0.014 0.001 PHE G 248 TYR 0.017 0.001 TYR G 507 ARG 0.002 0.000 ARG I 42 Details of bonding type rmsd hydrogen bonds : bond 0.14311 ( 1608) hydrogen bonds : angle 5.27937 ( 4524) metal coordination : bond 0.08175 ( 8) metal coordination : angle 2.87735 ( 6) covalent geometry : bond 0.00377 (34819) covalent geometry : angle 0.95548 (47111) Misc. bond : bond 0.52600 ( 3) *********************** 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 630 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 601 time to evaluate : 4.389 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 176 VAL cc_start: 0.7303 (t) cc_final: 0.7019 (t) REVERT: A 561 TRP cc_start: 0.3407 (t-100) cc_final: 0.3132 (t-100) REVERT: A 641 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: A 763 LYS cc_start: 0.7770 (mttt) cc_final: 0.7066 (tppt) REVERT: B 115 CYS cc_start: 0.3423 (t) cc_final: 0.3218 (t) REVERT: B 168 MET cc_start: 0.6819 (tpt) cc_final: 0.5415 (ppp) REVERT: B 341 LEU cc_start: 0.8851 (mt) cc_final: 0.8602 (mt) REVERT: B 784 MET cc_start: 0.6987 (mmm) cc_final: 0.6629 (tmm) REVERT: C 331 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 361 ASN cc_start: 0.8217 (t0) cc_final: 0.7914 (t0) REVERT: C 587 ASP cc_start: 0.7341 (t0) cc_final: 0.6743 (t0) REVERT: D 254 TYR cc_start: 0.8607 (p90) cc_final: 0.8342 (p90) REVERT: D 359 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7924 (mtp85) REVERT: D 361 ASN cc_start: 0.7405 (p0) cc_final: 0.6970 (p0) REVERT: D 515 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8555 (tmtt) REVERT: D 575 LYS cc_start: 0.8083 (mttt) cc_final: 0.7807 (mmmm) REVERT: D 646 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8039 (Cg_endo) REVERT: E 208 MET cc_start: 0.5902 (tpt) cc_final: 0.4939 (mpp) REVERT: E 339 LEU cc_start: 0.8933 (mp) cc_final: 0.8689 (mt) REVERT: E 644 LEU cc_start: 0.8823 (mm) cc_final: 0.8421 (pp) REVERT: E 775 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8345 (ttm110) REVERT: E 784 MET cc_start: 0.8073 (mmp) cc_final: 0.7660 (tmm) REVERT: F 587 ASP cc_start: 0.8303 (t0) cc_final: 0.7721 (t0) REVERT: F 753 ILE cc_start: 0.7468 (mp) cc_final: 0.7160 (mt) REVERT: G 208 HIS cc_start: 0.8681 (p-80) cc_final: 0.7960 (p-80) REVERT: G 211 TRP cc_start: 0.8497 (t-100) cc_final: 0.7915 (t-100) REVERT: G 218 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8377 (ptpp) REVERT: I 33 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7290 (mmmt) REVERT: K 204 PHE cc_start: 0.7715 (m-80) cc_final: 0.7367 (m-80) REVERT: K 205 VAL cc_start: 0.7821 (t) cc_final: 0.7612 (m) outliers start: 29 outliers final: 9 residues processed: 617 average time/residue: 0.5855 time to fit residues: 553.1728 Evaluate side-chains 336 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 327 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 502 GLN Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 264 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 4.9990 chunk 325 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 389 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 209 ASN C 612 ASN C 622 ASN D 100 ASN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS F 613 GLN F 670 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 497 GLN J 125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.131532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094128 restraints weight = 89510.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093528 restraints weight = 46623.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093776 restraints weight = 36780.747| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 34830 Z= 0.245 Angle : 0.715 10.148 47117 Z= 0.354 Chirality : 0.047 0.199 5306 Planarity : 0.005 0.046 6138 Dihedral : 11.222 154.823 4948 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 2.28 % Allowed : 9.18 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.13), residues: 4274 helix: 1.65 (0.12), residues: 2017 sheet: -0.31 (0.23), residues: 542 loop : -0.13 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 486 HIS 0.016 0.001 HIS F 509 PHE 0.020 0.002 PHE G 248 TYR 0.031 0.002 TYR G 507 ARG 0.010 0.001 ARG E 323 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1608) hydrogen bonds : angle 4.77535 ( 4524) metal coordination : bond 0.03506 ( 8) metal coordination : angle 2.92033 ( 6) covalent geometry : bond 0.00581 (34819) covalent geometry : angle 0.71416 (47111) Misc. bond : bond 0.00249 ( 3) *********************** 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 431 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 4.168 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 323 ARG cc_start: 0.8332 (ttt180) cc_final: 0.7748 (tpp-160) REVERT: A 699 TYR cc_start: 0.7882 (t80) cc_final: 0.7674 (t80) REVERT: A 706 LYS cc_start: 0.9314 (ttmm) cc_final: 0.9114 (pttt) REVERT: A 763 LYS cc_start: 0.7583 (mttt) cc_final: 0.7232 (tppt) REVERT: B 37 LEU cc_start: 0.8697 (mp) cc_final: 0.8423 (pp) REVERT: B 113 HIS cc_start: 0.7341 (t70) cc_final: 0.6865 (t-90) REVERT: B 168 MET cc_start: 0.7105 (tpt) cc_final: 0.5609 (ppp) REVERT: B 480 GLU cc_start: 0.8441 (pm20) cc_final: 0.8061 (pm20) REVERT: B 552 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 784 MET cc_start: 0.7349 (mmm) cc_final: 0.6885 (tmm) REVERT: C 285 MET cc_start: 0.8595 (mmm) cc_final: 0.8336 (mmm) REVERT: C 288 MET cc_start: 0.8446 (tpp) cc_final: 0.8243 (tpp) REVERT: C 331 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 361 ASN cc_start: 0.8351 (t0) cc_final: 0.8005 (t0) REVERT: C 618 MET cc_start: 0.8477 (tmm) cc_final: 0.7897 (tmm) REVERT: C 699 TYR cc_start: 0.9039 (t80) cc_final: 0.8797 (t80) REVERT: D 100 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7437 (p0) REVERT: D 254 TYR cc_start: 0.8894 (p90) cc_final: 0.8691 (p90) REVERT: D 285 MET cc_start: 0.8371 (tpp) cc_final: 0.7939 (tmm) REVERT: D 359 ARG cc_start: 0.8431 (mtm110) cc_final: 0.7984 (mtp85) REVERT: D 361 ASN cc_start: 0.7547 (p0) cc_final: 0.7006 (p0) REVERT: D 646 PRO cc_start: 0.8491 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: E 208 MET cc_start: 0.6350 (tpt) cc_final: 0.5134 (mpp) REVERT: E 282 PRO cc_start: 0.7565 (Cg_exo) cc_final: 0.7277 (Cg_endo) REVERT: E 775 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8229 (ttm110) REVERT: E 784 MET cc_start: 0.8129 (mmp) cc_final: 0.7900 (mmp) REVERT: F 775 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8662 (mmp80) REVERT: G 218 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8429 (ptpp) REVERT: I 33 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7323 (mmmt) REVERT: I 39 ASP cc_start: 0.8131 (t0) cc_final: 0.7908 (t0) REVERT: K 204 PHE cc_start: 0.8212 (m-80) cc_final: 0.7506 (m-10) outliers start: 84 outliers final: 36 residues processed: 410 average time/residue: 0.5121 time to fit residues: 341.7149 Evaluate side-chains 323 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 6.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 490 SER Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 229 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 336 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 chunk 349 optimal weight: 0.9980 chunk 422 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN B 638 GLN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 461 ASN E 509 HIS F 238 GLN F 358 ASN ** F 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN K 268 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.133919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096232 restraints weight = 89623.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096490 restraints weight = 55855.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096520 restraints weight = 37278.701| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34830 Z= 0.128 Angle : 0.612 8.782 47117 Z= 0.297 Chirality : 0.043 0.159 5306 Planarity : 0.004 0.052 6138 Dihedral : 10.585 148.540 4937 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 1.74 % Allowed : 11.06 % Favored : 87.20 % 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: 1.08 (0.13), residues: 4274 helix: 1.73 (0.12), residues: 2009 sheet: -0.16 (0.23), residues: 542 loop : -0.12 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 252 HIS 0.020 0.001 HIS F 509 PHE 0.014 0.001 PHE G 248 TYR 0.023 0.001 TYR G 507 ARG 0.008 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 1608) hydrogen bonds : angle 4.40544 ( 4524) metal coordination : bond 0.00972 ( 8) metal coordination : angle 2.07622 ( 6) covalent geometry : bond 0.00286 (34819) covalent geometry : angle 0.61142 (47111) Misc. bond : bond 0.00201 ( 3) *********************** 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 391 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 327 time to evaluate : 4.908 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 285 MET cc_start: 0.8079 (mmp) cc_final: 0.7842 (mmm) REVERT: A 323 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7663 (tpp-160) REVERT: A 619 ASP cc_start: 0.8917 (t0) cc_final: 0.8701 (t0) REVERT: A 763 LYS cc_start: 0.7480 (mttt) cc_final: 0.7194 (tppt) REVERT: B 24 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8472 (t) REVERT: B 113 HIS cc_start: 0.7186 (t70) cc_final: 0.6919 (t-90) REVERT: B 168 MET cc_start: 0.7304 (tpt) cc_final: 0.5835 (ppp) REVERT: B 183 TYR cc_start: 0.5826 (p90) cc_final: 0.5244 (p90) REVERT: B 345 MET cc_start: 0.8373 (ptm) cc_final: 0.8037 (ttp) REVERT: B 480 GLU cc_start: 0.8467 (pm20) cc_final: 0.8025 (pm20) REVERT: B 784 MET cc_start: 0.7529 (mmm) cc_final: 0.7121 (tmm) REVERT: C 285 MET cc_start: 0.8484 (mmm) cc_final: 0.8194 (mmm) REVERT: C 288 MET cc_start: 0.8417 (tpp) cc_final: 0.8206 (tpp) REVERT: C 331 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 361 ASN cc_start: 0.8226 (t0) cc_final: 0.8009 (t0) REVERT: C 561 TRP cc_start: 0.7315 (t60) cc_final: 0.6959 (t60) REVERT: C 618 MET cc_start: 0.8320 (tmm) cc_final: 0.7772 (tmm) REVERT: C 699 TYR cc_start: 0.9068 (t80) cc_final: 0.8836 (t80) REVERT: D 75 LYS cc_start: 0.7661 (mmmm) cc_final: 0.7107 (tptt) REVERT: D 285 MET cc_start: 0.8458 (tpp) cc_final: 0.8013 (tmm) REVERT: D 301 GLU cc_start: 0.8223 (tp30) cc_final: 0.7928 (tp30) REVERT: D 359 ARG cc_start: 0.8292 (mtm110) cc_final: 0.7963 (mtp85) REVERT: D 646 PRO cc_start: 0.8524 (Cg_exo) cc_final: 0.8207 (Cg_endo) REVERT: E 208 MET cc_start: 0.6576 (tpt) cc_final: 0.5274 (mpp) REVERT: E 282 PRO cc_start: 0.7188 (Cg_exo) cc_final: 0.6913 (Cg_endo) REVERT: E 324 ASP cc_start: 0.8922 (m-30) cc_final: 0.8594 (m-30) REVERT: E 676 LEU cc_start: 0.8628 (pt) cc_final: 0.8026 (tp) REVERT: E 762 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6623 (tpp) REVERT: E 775 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8193 (ttm110) REVERT: E 784 MET cc_start: 0.8166 (mmp) cc_final: 0.7894 (mmp) REVERT: F 280 ASN cc_start: 0.7484 (m-40) cc_final: 0.7231 (t0) REVERT: G 190 ILE cc_start: 0.8430 (mm) cc_final: 0.8228 (mm) REVERT: G 218 LYS cc_start: 0.8831 (ptmt) cc_final: 0.8423 (ptpp) REVERT: G 574 MET cc_start: 0.8015 (tpt) cc_final: 0.7391 (tpt) REVERT: I 33 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7123 (mmmt) REVERT: I 39 ASP cc_start: 0.8135 (t0) cc_final: 0.7915 (t0) REVERT: K 204 PHE cc_start: 0.8179 (m-80) cc_final: 0.7622 (m-80) REVERT: K 234 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7653 (tp30) outliers start: 64 outliers final: 37 residues processed: 377 average time/residue: 0.5311 time to fit residues: 330.6528 Evaluate side-chains 329 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 490 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 234 GLU Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 363 optimal weight: 0.3980 chunk 303 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 414 optimal weight: 0.0060 chunk 269 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN B 638 GLN D 100 ASN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.130439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095264 restraints weight = 89443.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094168 restraints weight = 45529.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095090 restraints weight = 33965.099| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34830 Z= 0.137 Angle : 0.598 8.595 47117 Z= 0.288 Chirality : 0.042 0.172 5306 Planarity : 0.004 0.055 6138 Dihedral : 10.107 144.971 4934 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 2.04 % Allowed : 11.74 % Favored : 86.22 % 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: 1.09 (0.13), residues: 4274 helix: 1.73 (0.12), residues: 2009 sheet: -0.17 (0.23), residues: 550 loop : -0.10 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 252 HIS 0.011 0.001 HIS E 509 PHE 0.014 0.001 PHE G 248 TYR 0.022 0.001 TYR G 507 ARG 0.015 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1608) hydrogen bonds : angle 4.32704 ( 4524) metal coordination : bond 0.01327 ( 8) metal coordination : angle 1.93145 ( 6) covalent geometry : bond 0.00317 (34819) covalent geometry : angle 0.59773 (47111) Misc. bond : bond 0.00063 ( 3) *********************** 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 379 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 304 time to evaluate : 4.239 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 285 MET cc_start: 0.8172 (mmp) cc_final: 0.7840 (mmm) REVERT: A 323 ARG cc_start: 0.8304 (ttt180) cc_final: 0.7834 (tpp-160) REVERT: B 24 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8653 (t) REVERT: B 113 HIS cc_start: 0.7193 (t70) cc_final: 0.6851 (t-90) REVERT: B 168 MET cc_start: 0.7163 (tpt) cc_final: 0.5829 (ppp) REVERT: B 183 TYR cc_start: 0.5826 (p90) cc_final: 0.5585 (p90) REVERT: B 345 MET cc_start: 0.8341 (ptm) cc_final: 0.8062 (ttp) REVERT: B 480 GLU cc_start: 0.8405 (pm20) cc_final: 0.7964 (pm20) REVERT: B 588 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7621 (mm-30) REVERT: B 784 MET cc_start: 0.7532 (mmm) cc_final: 0.7158 (tmm) REVERT: C 285 MET cc_start: 0.8467 (mmm) cc_final: 0.8191 (mmm) REVERT: C 298 LYS cc_start: 0.8525 (mttt) cc_final: 0.7841 (pttp) REVERT: C 331 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7802 (mt-10) REVERT: C 361 ASN cc_start: 0.8247 (t0) cc_final: 0.7937 (t0) REVERT: C 561 TRP cc_start: 0.7447 (t60) cc_final: 0.7193 (t60) REVERT: C 618 MET cc_start: 0.8248 (tmm) cc_final: 0.7865 (tmm) REVERT: C 699 TYR cc_start: 0.9019 (t80) cc_final: 0.8792 (t80) REVERT: D 75 LYS cc_start: 0.7557 (mmmm) cc_final: 0.7061 (tptt) REVERT: D 285 MET cc_start: 0.8402 (tpp) cc_final: 0.8000 (tmm) REVERT: D 301 GLU cc_start: 0.8284 (tp30) cc_final: 0.7933 (tp30) REVERT: D 359 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8007 (mtp85) REVERT: D 646 PRO cc_start: 0.8365 (Cg_exo) cc_final: 0.8033 (Cg_endo) REVERT: E 208 MET cc_start: 0.6634 (tpt) cc_final: 0.5343 (mpp) REVERT: E 223 MET cc_start: 0.8182 (tpp) cc_final: 0.7840 (tpp) REVERT: E 282 PRO cc_start: 0.7022 (Cg_exo) cc_final: 0.6715 (Cg_endo) REVERT: E 324 ASP cc_start: 0.8931 (m-30) cc_final: 0.8648 (m-30) REVERT: E 345 MET cc_start: 0.7863 (mmm) cc_final: 0.7630 (tpp) REVERT: E 573 PHE cc_start: 0.9105 (m-80) cc_final: 0.8879 (m-80) REVERT: E 676 LEU cc_start: 0.8592 (pt) cc_final: 0.8002 (tp) REVERT: E 762 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6616 (tpp) REVERT: E 775 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.8199 (ttm110) REVERT: E 784 MET cc_start: 0.8127 (mmp) cc_final: 0.7903 (mmp) REVERT: F 223 MET cc_start: 0.9211 (mmm) cc_final: 0.8844 (mmm) REVERT: F 254 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7351 (p90) REVERT: F 280 ASN cc_start: 0.7558 (m-40) cc_final: 0.7276 (t0) REVERT: G 213 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7817 (mtt-85) REVERT: G 218 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8416 (ptpp) REVERT: G 574 MET cc_start: 0.8063 (tpt) cc_final: 0.7574 (tpt) REVERT: I 33 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7142 (mmmt) REVERT: K 204 PHE cc_start: 0.8074 (m-80) cc_final: 0.7590 (m-80) outliers start: 75 outliers final: 45 residues processed: 364 average time/residue: 0.4766 time to fit residues: 285.0602 Evaluate side-chains 325 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 490 SER Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 3.9990 chunk 374 optimal weight: 0.4980 chunk 87 optimal weight: 0.0570 chunk 112 optimal weight: 0.0980 chunk 119 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 37 optimal weight: 0.0970 chunk 93 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN D 295 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN I 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.135490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098704 restraints weight = 89367.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098583 restraints weight = 44409.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099039 restraints weight = 32926.126| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34830 Z= 0.102 Angle : 0.587 11.487 47117 Z= 0.279 Chirality : 0.042 0.190 5306 Planarity : 0.004 0.055 6138 Dihedral : 9.357 138.889 4933 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 1.52 % Allowed : 12.66 % Favored : 85.82 % 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: 1.22 (0.14), residues: 4274 helix: 1.79 (0.12), residues: 2025 sheet: 0.03 (0.23), residues: 546 loop : -0.02 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 252 HIS 0.008 0.001 HIS G 208 PHE 0.015 0.001 PHE E 628 TYR 0.019 0.001 TYR E 254 ARG 0.006 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 1608) hydrogen bonds : angle 4.10711 ( 4524) metal coordination : bond 0.00458 ( 8) metal coordination : angle 2.30690 ( 6) covalent geometry : bond 0.00215 (34819) covalent geometry : angle 0.58685 (47111) Misc. bond : bond 0.00032 ( 3) *********************** 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 382 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 326 time to evaluate : 3.742 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 165 ARG cc_start: 0.6288 (mpp-170) cc_final: 0.4544 (tpp80) REVERT: A 229 MET cc_start: 0.8401 (tpp) cc_final: 0.7566 (mmt) REVERT: A 285 MET cc_start: 0.8165 (mmp) cc_final: 0.7758 (mmm) REVERT: A 323 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7459 (mmm-85) REVERT: A 784 MET cc_start: 0.8339 (mmm) cc_final: 0.8111 (mmp) REVERT: B 24 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8574 (t) REVERT: B 113 HIS cc_start: 0.6966 (t70) cc_final: 0.6625 (t-90) REVERT: B 168 MET cc_start: 0.7274 (tpt) cc_final: 0.6018 (ppp) REVERT: B 183 TYR cc_start: 0.6114 (p90) cc_final: 0.5509 (p90) REVERT: B 208 MET cc_start: 0.6783 (mmm) cc_final: 0.6534 (mmm) REVERT: B 345 MET cc_start: 0.8171 (ptm) cc_final: 0.7966 (ttp) REVERT: B 480 GLU cc_start: 0.8304 (pm20) cc_final: 0.7840 (pm20) REVERT: B 588 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7564 (mm-30) REVERT: B 784 MET cc_start: 0.7550 (mmm) cc_final: 0.7204 (tmm) REVERT: C 285 MET cc_start: 0.8523 (mmm) cc_final: 0.8219 (mmm) REVERT: C 298 LYS cc_start: 0.8421 (mttt) cc_final: 0.7805 (pttp) REVERT: C 574 ASP cc_start: 0.8184 (t0) cc_final: 0.7850 (t0) REVERT: C 618 MET cc_start: 0.8189 (tmm) cc_final: 0.7836 (tmm) REVERT: C 699 TYR cc_start: 0.9078 (t80) cc_final: 0.8872 (t80) REVERT: D 75 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7157 (tptt) REVERT: D 285 MET cc_start: 0.8380 (tpp) cc_final: 0.7987 (tmm) REVERT: D 301 GLU cc_start: 0.8258 (tp30) cc_final: 0.7903 (tp30) REVERT: D 359 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7914 (mtp85) REVERT: D 646 PRO cc_start: 0.8380 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: E 208 MET cc_start: 0.6640 (tpt) cc_final: 0.5319 (mpp) REVERT: E 282 PRO cc_start: 0.6968 (Cg_exo) cc_final: 0.6654 (Cg_endo) REVERT: E 324 ASP cc_start: 0.8925 (m-30) cc_final: 0.8634 (m-30) REVERT: E 345 MET cc_start: 0.7971 (mmm) cc_final: 0.7727 (tpp) REVERT: E 573 PHE cc_start: 0.9113 (m-80) cc_final: 0.8866 (m-80) REVERT: E 676 LEU cc_start: 0.8587 (pt) cc_final: 0.7978 (tp) REVERT: E 762 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6656 (tpp) REVERT: E 775 ARG cc_start: 0.8709 (tmm-80) cc_final: 0.8195 (ttm110) REVERT: E 784 MET cc_start: 0.8142 (mmp) cc_final: 0.7895 (mmp) REVERT: F 223 MET cc_start: 0.9250 (mmm) cc_final: 0.8816 (mmm) REVERT: F 280 ASN cc_start: 0.7512 (m-40) cc_final: 0.7211 (t0) REVERT: G 218 LYS cc_start: 0.8831 (ptmt) cc_final: 0.8395 (ptpp) REVERT: G 574 MET cc_start: 0.8029 (tpt) cc_final: 0.7621 (tpt) REVERT: I 33 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7081 (mmmt) REVERT: K 204 PHE cc_start: 0.8078 (m-80) cc_final: 0.7526 (m-80) outliers start: 56 outliers final: 34 residues processed: 368 average time/residue: 0.5733 time to fit residues: 348.6635 Evaluate side-chains 323 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 312 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 282 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 124 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 638 GLN B 718 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 295 ASN E 509 HIS F 548 ASN F 634 ASN G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN I 40 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.127843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089643 restraints weight = 88865.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090046 restraints weight = 49725.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090758 restraints weight = 33737.805| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 34830 Z= 0.291 Angle : 0.710 11.009 47117 Z= 0.350 Chirality : 0.046 0.211 5306 Planarity : 0.004 0.061 6138 Dihedral : 9.385 140.033 4933 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.58 % Allowed : 12.93 % Favored : 84.48 % 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: 0.91 (0.13), residues: 4274 helix: 1.58 (0.12), residues: 2008 sheet: -0.22 (0.23), residues: 530 loop : -0.19 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 561 HIS 0.011 0.002 HIS G 290 PHE 0.019 0.002 PHE G 248 TYR 0.034 0.002 TYR G 189 ARG 0.007 0.001 ARG E 672 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1608) hydrogen bonds : angle 4.56919 ( 4524) metal coordination : bond 0.03621 ( 8) metal coordination : angle 2.53243 ( 6) covalent geometry : bond 0.00686 (34819) covalent geometry : angle 0.70993 (47111) Misc. bond : bond 0.00111 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 280 time to evaluate : 8.878 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 165 ARG cc_start: 0.6358 (mpp-170) cc_final: 0.4924 (tpp80) REVERT: B 24 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8718 (t) REVERT: B 113 HIS cc_start: 0.7056 (t70) cc_final: 0.6669 (t-90) REVERT: B 168 MET cc_start: 0.7395 (tpt) cc_final: 0.6050 (ppp) REVERT: B 223 MET cc_start: 0.8696 (mmm) cc_final: 0.8363 (tpt) REVERT: B 254 TYR cc_start: 0.8691 (p90) cc_final: 0.8471 (p90) REVERT: B 480 GLU cc_start: 0.8433 (pm20) cc_final: 0.7927 (pm20) REVERT: B 784 MET cc_start: 0.7479 (mmm) cc_final: 0.7196 (tmm) REVERT: C 285 MET cc_start: 0.8550 (mmm) cc_final: 0.8242 (mmm) REVERT: C 331 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 618 MET cc_start: 0.8003 (tmm) cc_final: 0.7590 (tmm) REVERT: D 301 GLU cc_start: 0.8412 (tp30) cc_final: 0.8005 (tp30) REVERT: D 314 ASP cc_start: 0.8311 (t0) cc_final: 0.8101 (t0) REVERT: D 359 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8001 (mtp85) REVERT: D 575 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8080 (mmmm) REVERT: D 646 PRO cc_start: 0.8498 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: E 208 MET cc_start: 0.6710 (tpt) cc_final: 0.5390 (mpp) REVERT: E 282 PRO cc_start: 0.7344 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: E 345 MET cc_start: 0.8044 (mmm) cc_final: 0.7688 (tpp) REVERT: E 676 LEU cc_start: 0.8639 (pt) cc_final: 0.8059 (tp) REVERT: E 762 MET cc_start: 0.7334 (tpt) cc_final: 0.6663 (tpp) REVERT: E 775 ARG cc_start: 0.8650 (tmm-80) cc_final: 0.8159 (ttm110) REVERT: E 784 MET cc_start: 0.8228 (mmp) cc_final: 0.7960 (mmp) REVERT: F 254 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7702 (p90) REVERT: G 133 LYS cc_start: 0.8463 (tmtt) cc_final: 0.8253 (tppt) REVERT: G 218 LYS cc_start: 0.8961 (ptmt) cc_final: 0.8518 (ptpp) REVERT: G 574 MET cc_start: 0.8110 (tpt) cc_final: 0.7685 (tpt) REVERT: I 33 LYS cc_start: 0.8514 (mtmm) cc_final: 0.7496 (mmmt) REVERT: K 204 PHE cc_start: 0.8098 (m-80) cc_final: 0.7610 (m-10) outliers start: 95 outliers final: 62 residues processed: 359 average time/residue: 0.7295 time to fit residues: 441.1893 Evaluate side-chains 321 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 709 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 390 LEU 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 526 ASN Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 241 GLN Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 248 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 400 optimal weight: 1.9990 chunk 384 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 chunk 374 optimal weight: 0.5980 chunk 263 optimal weight: 0.3980 chunk 222 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 718 GLN C 361 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.132972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096246 restraints weight = 89024.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095755 restraints weight = 46419.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096145 restraints weight = 35810.311| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34830 Z= 0.113 Angle : 0.609 9.827 47117 Z= 0.291 Chirality : 0.042 0.184 5306 Planarity : 0.004 0.058 6138 Dihedral : 8.853 135.503 4933 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.58 % Allowed : 14.27 % Favored : 84.16 % 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: 1.10 (0.14), residues: 4274 helix: 1.74 (0.12), residues: 2016 sheet: -0.10 (0.23), residues: 539 loop : -0.11 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 561 HIS 0.018 0.001 HIS E 509 PHE 0.012 0.001 PHE G 248 TYR 0.022 0.001 TYR G 507 ARG 0.004 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1608) hydrogen bonds : angle 4.26739 ( 4524) metal coordination : bond 0.01372 ( 8) metal coordination : angle 2.70371 ( 6) covalent geometry : bond 0.00249 (34819) covalent geometry : angle 0.60777 (47111) Misc. bond : bond 0.00034 ( 3) *********************** 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 346 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 4.478 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 165 ARG cc_start: 0.6329 (mpp-170) cc_final: 0.4906 (tpp80) REVERT: A 208 MET cc_start: 0.8414 (ttt) cc_final: 0.8139 (ttp) REVERT: A 245 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8904 (pt) REVERT: A 285 MET cc_start: 0.8166 (mmm) cc_final: 0.7845 (mmm) REVERT: A 459 MET cc_start: 0.8303 (tpt) cc_final: 0.7875 (tpp) REVERT: B 24 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (t) REVERT: B 113 HIS cc_start: 0.7259 (t70) cc_final: 0.6835 (t-90) REVERT: B 168 MET cc_start: 0.7559 (tpt) cc_final: 0.6246 (ppp) REVERT: B 183 TYR cc_start: 0.6258 (p90) cc_final: 0.5655 (p90) REVERT: B 223 MET cc_start: 0.8656 (mmm) cc_final: 0.8249 (tpt) REVERT: B 480 GLU cc_start: 0.8358 (pm20) cc_final: 0.7837 (pm20) REVERT: B 784 MET cc_start: 0.7754 (mmm) cc_final: 0.7352 (tmm) REVERT: C 285 MET cc_start: 0.8497 (mmm) cc_final: 0.8194 (mmm) REVERT: C 329 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: C 331 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 618 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7686 (tmm) REVERT: D 75 LYS cc_start: 0.7555 (mmmm) cc_final: 0.7041 (tptt) REVERT: D 285 MET cc_start: 0.8404 (tpp) cc_final: 0.7996 (tmm) REVERT: D 301 GLU cc_start: 0.8345 (tp30) cc_final: 0.8005 (tp30) REVERT: D 359 ARG cc_start: 0.8457 (mtm110) cc_final: 0.7979 (mtp85) REVERT: D 646 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8257 (Cg_endo) REVERT: E 208 MET cc_start: 0.6719 (tpt) cc_final: 0.5380 (mpp) REVERT: E 282 PRO cc_start: 0.7212 (Cg_exo) cc_final: 0.6867 (Cg_endo) REVERT: E 573 PHE cc_start: 0.9117 (m-80) cc_final: 0.8807 (m-80) REVERT: E 676 LEU cc_start: 0.8623 (pt) cc_final: 0.8040 (tp) REVERT: E 762 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6614 (tpp) REVERT: E 775 ARG cc_start: 0.8630 (tmm-80) cc_final: 0.8134 (ttm110) REVERT: E 784 MET cc_start: 0.8225 (mmp) cc_final: 0.7916 (mmp) REVERT: G 213 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7827 (mtt-85) REVERT: G 218 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8425 (ptpp) REVERT: G 574 MET cc_start: 0.8062 (tpt) cc_final: 0.7675 (tpt) REVERT: I 33 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7190 (mmmt) REVERT: K 204 PHE cc_start: 0.8104 (m-80) cc_final: 0.7386 (m-10) outliers start: 58 outliers final: 40 residues processed: 335 average time/residue: 0.4811 time to fit residues: 264.8665 Evaluate side-chains 317 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 709 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN C 361 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 HIS E 638 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN G 570 GLN K 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094535 restraints weight = 89178.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.093591 restraints weight = 47963.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093813 restraints weight = 36788.985| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34830 Z= 0.207 Angle : 0.654 10.133 47117 Z= 0.317 Chirality : 0.044 0.216 5306 Planarity : 0.004 0.061 6138 Dihedral : 8.777 134.562 4933 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 1.68 % Allowed : 14.70 % Favored : 83.61 % 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: 0.99 (0.13), residues: 4274 helix: 1.66 (0.12), residues: 2009 sheet: -0.21 (0.23), residues: 536 loop : -0.16 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP C 561 HIS 0.007 0.001 HIS G 290 PHE 0.017 0.001 PHE G 248 TYR 0.024 0.001 TYR G 507 ARG 0.005 0.000 ARG E 672 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1608) hydrogen bonds : angle 4.42131 ( 4524) metal coordination : bond 0.02707 ( 8) metal coordination : angle 2.67766 ( 6) covalent geometry : bond 0.00489 (34819) covalent geometry : angle 0.65360 (47111) Misc. bond : bond 0.00072 ( 3) *********************** 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 333 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 3.986 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 165 ARG cc_start: 0.6334 (mpp-170) cc_final: 0.5708 (mpt-90) REVERT: A 223 MET cc_start: 0.9138 (mmm) cc_final: 0.8936 (tpp) REVERT: A 245 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8968 (pt) REVERT: A 285 MET cc_start: 0.8224 (mmm) cc_final: 0.7872 (mmm) REVERT: B 113 HIS cc_start: 0.7274 (t70) cc_final: 0.6837 (t-90) REVERT: B 168 MET cc_start: 0.7534 (tpt) cc_final: 0.6211 (ppp) REVERT: B 480 GLU cc_start: 0.8404 (pm20) cc_final: 0.7860 (pm20) REVERT: B 784 MET cc_start: 0.7719 (mmm) cc_final: 0.7379 (tmm) REVERT: C 329 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: C 331 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 618 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7655 (tmm) REVERT: D 359 ARG cc_start: 0.8434 (mtm110) cc_final: 0.7994 (mtp85) REVERT: D 564 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: D 646 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8339 (Cg_endo) REVERT: E 208 MET cc_start: 0.6753 (tpt) cc_final: 0.5421 (mpp) REVERT: E 282 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.6943 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8661 (pt) cc_final: 0.8083 (tp) REVERT: E 762 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6587 (tpp) REVERT: E 775 ARG cc_start: 0.8631 (tmm-80) cc_final: 0.8138 (ttm110) REVERT: E 784 MET cc_start: 0.8212 (mmp) cc_final: 0.7900 (mmp) REVERT: F 325 LYS cc_start: 0.7848 (tmtt) cc_final: 0.7616 (tmtt) REVERT: G 133 LYS cc_start: 0.8444 (tmtt) cc_final: 0.8238 (tppt) REVERT: G 218 LYS cc_start: 0.8918 (ptmt) cc_final: 0.8476 (ptpp) REVERT: G 574 MET cc_start: 0.7985 (tpt) cc_final: 0.7605 (tpt) REVERT: I 33 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7337 (mmmt) REVERT: K 204 PHE cc_start: 0.8124 (m-80) cc_final: 0.7609 (m-80) outliers start: 62 outliers final: 41 residues processed: 321 average time/residue: 0.4904 time to fit residues: 259.2340 Evaluate side-chains 309 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 709 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 393 optimal weight: 0.8980 chunk 317 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 718 GLN C 361 ASN E 509 HIS E 638 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.130168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095198 restraints weight = 89157.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093964 restraints weight = 46178.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094335 restraints weight = 36951.702| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34830 Z= 0.121 Angle : 0.617 10.637 47117 Z= 0.294 Chirality : 0.042 0.170 5306 Planarity : 0.004 0.059 6138 Dihedral : 8.501 131.586 4933 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 1.88 % Allowed : 14.97 % Favored : 83.15 % 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: 1.12 (0.14), residues: 4274 helix: 1.75 (0.12), residues: 2006 sheet: -0.14 (0.23), residues: 540 loop : -0.08 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP C 561 HIS 0.012 0.001 HIS E 509 PHE 0.014 0.001 PHE G 517 TYR 0.021 0.001 TYR G 507 ARG 0.004 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1608) hydrogen bonds : angle 4.27184 ( 4524) metal coordination : bond 0.01267 ( 8) metal coordination : angle 2.54280 ( 6) covalent geometry : bond 0.00274 (34819) covalent geometry : angle 0.61617 (47111) Misc. bond : bond 0.00030 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 3.721 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 165 ARG cc_start: 0.6423 (mpp-170) cc_final: 0.5832 (mpt-90) REVERT: A 223 MET cc_start: 0.9151 (mmm) cc_final: 0.8932 (tpp) REVERT: A 245 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8973 (pt) REVERT: A 285 MET cc_start: 0.8147 (mmm) cc_final: 0.7826 (mmm) REVERT: A 437 MET cc_start: 0.7705 (ppp) cc_final: 0.7360 (ttm) REVERT: A 459 MET cc_start: 0.8400 (tpt) cc_final: 0.7966 (tpp) REVERT: B 113 HIS cc_start: 0.7331 (t70) cc_final: 0.6888 (t-90) REVERT: B 168 MET cc_start: 0.7526 (tpt) cc_final: 0.6294 (ppp) REVERT: B 480 GLU cc_start: 0.8353 (pm20) cc_final: 0.7827 (pm20) REVERT: B 784 MET cc_start: 0.7712 (mmm) cc_final: 0.7356 (tmm) REVERT: C 285 MET cc_start: 0.8425 (mmm) cc_final: 0.8134 (mmm) REVERT: C 329 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: C 331 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 618 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7737 (tmm) REVERT: C 619 ASP cc_start: 0.8274 (t0) cc_final: 0.7920 (m-30) REVERT: D 75 LYS cc_start: 0.7466 (mmmm) cc_final: 0.6972 (tptt) REVERT: D 359 ARG cc_start: 0.8437 (mtm110) cc_final: 0.7937 (mtp85) REVERT: D 564 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: E 208 MET cc_start: 0.6735 (tpt) cc_final: 0.5289 (mpp) REVERT: E 282 PRO cc_start: 0.7265 (Cg_exo) cc_final: 0.6926 (Cg_endo) REVERT: E 573 PHE cc_start: 0.9245 (m-80) cc_final: 0.8912 (m-80) REVERT: E 676 LEU cc_start: 0.8651 (pt) cc_final: 0.8074 (tp) REVERT: E 762 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6589 (tpp) REVERT: E 775 ARG cc_start: 0.8629 (tmm-80) cc_final: 0.8155 (ttm110) REVERT: E 784 MET cc_start: 0.8220 (mmp) cc_final: 0.7907 (mmp) REVERT: F 325 LYS cc_start: 0.7835 (tmtt) cc_final: 0.7581 (tmtt) REVERT: G 213 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7748 (mtt-85) REVERT: G 218 LYS cc_start: 0.8889 (ptmt) cc_final: 0.8454 (ptpp) REVERT: G 574 MET cc_start: 0.8023 (tpt) cc_final: 0.7656 (tpt) REVERT: I 33 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7253 (mmmt) REVERT: K 204 PHE cc_start: 0.7873 (m-80) cc_final: 0.7401 (m-80) outliers start: 69 outliers final: 43 residues processed: 332 average time/residue: 0.4484 time to fit residues: 244.3697 Evaluate side-chains 319 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 709 ILE Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 320 optimal weight: 0.3980 chunk 206 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 408 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 395 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 361 ASN E 638 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095302 restraints weight = 88803.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094242 restraints weight = 45988.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094628 restraints weight = 36195.508| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34830 Z= 0.125 Angle : 0.617 13.625 47117 Z= 0.293 Chirality : 0.042 0.162 5306 Planarity : 0.004 0.060 6138 Dihedral : 8.265 128.670 4933 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.39 % Allowed : 15.35 % Favored : 83.26 % 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: 1.16 (0.14), residues: 4274 helix: 1.77 (0.12), residues: 2007 sheet: -0.06 (0.23), residues: 543 loop : -0.05 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 252 HIS 0.003 0.001 HIS G 521 PHE 0.024 0.001 PHE F 758 TYR 0.027 0.001 TYR G 507 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1608) hydrogen bonds : angle 4.23887 ( 4524) metal coordination : bond 0.01298 ( 8) metal coordination : angle 2.52827 ( 6) covalent geometry : bond 0.00287 (34819) covalent geometry : angle 0.61598 (47111) Misc. bond : bond 0.00037 ( 3) ********************** 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 329 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 4.017 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 165 ARG cc_start: 0.6485 (mpp-170) cc_final: 0.5849 (mpt-90) REVERT: A 229 MET cc_start: 0.8231 (mtp) cc_final: 0.7974 (mtp) REVERT: A 245 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8989 (pt) REVERT: A 285 MET cc_start: 0.8167 (mmm) cc_final: 0.7842 (mmm) REVERT: A 459 MET cc_start: 0.8381 (tpt) cc_final: 0.7959 (tpp) REVERT: A 780 TYR cc_start: 0.8207 (t80) cc_final: 0.8004 (t80) REVERT: B 113 HIS cc_start: 0.7340 (t70) cc_final: 0.6884 (t-90) REVERT: B 168 MET cc_start: 0.7525 (tpt) cc_final: 0.6326 (ppp) REVERT: B 480 GLU cc_start: 0.8326 (pm20) cc_final: 0.7804 (pm20) REVERT: B 784 MET cc_start: 0.7686 (mmm) cc_final: 0.7356 (tmm) REVERT: C 285 MET cc_start: 0.8418 (mmm) cc_final: 0.8122 (mmm) REVERT: C 329 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: C 331 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7831 (mt-10) REVERT: C 342 MET cc_start: 0.8773 (mmm) cc_final: 0.8535 (mmm) REVERT: C 618 MET cc_start: 0.8163 (tmm) cc_final: 0.7780 (tmm) REVERT: C 619 ASP cc_start: 0.8278 (t0) cc_final: 0.7929 (m-30) REVERT: C 784 MET cc_start: 0.6287 (mmp) cc_final: 0.6039 (mmm) REVERT: D 75 LYS cc_start: 0.7311 (mmmm) cc_final: 0.6902 (tptt) REVERT: D 359 ARG cc_start: 0.8463 (mtm110) cc_final: 0.7913 (mtp85) REVERT: D 564 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: E 208 MET cc_start: 0.6726 (tpt) cc_final: 0.5298 (mpp) REVERT: E 223 MET cc_start: 0.8335 (tpp) cc_final: 0.8054 (tpp) REVERT: E 282 PRO cc_start: 0.7228 (Cg_exo) cc_final: 0.6876 (Cg_endo) REVERT: E 573 PHE cc_start: 0.9205 (m-80) cc_final: 0.8866 (m-80) REVERT: E 676 LEU cc_start: 0.8648 (pt) cc_final: 0.8073 (tp) REVERT: E 762 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6601 (tpp) REVERT: E 775 ARG cc_start: 0.8631 (tmm-80) cc_final: 0.8157 (ttm110) REVERT: E 784 MET cc_start: 0.8226 (mmp) cc_final: 0.7910 (mmp) REVERT: F 325 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7583 (tmtt) REVERT: G 133 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8126 (tppt) REVERT: G 218 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8454 (ptpp) REVERT: G 574 MET cc_start: 0.8031 (tpt) cc_final: 0.7674 (tpt) REVERT: I 33 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7246 (mmmt) REVERT: K 204 PHE cc_start: 0.7867 (m-80) cc_final: 0.7598 (m-80) outliers start: 51 outliers final: 42 residues processed: 318 average time/residue: 0.4658 time to fit residues: 244.6271 Evaluate side-chains 318 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 709 ILE Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 426 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 0.0770 chunk 334 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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** B 718 GLN C 361 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.131795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093728 restraints weight = 89316.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094295 restraints weight = 48837.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094353 restraints weight = 34705.116| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34830 Z= 0.155 Angle : 0.632 16.666 47117 Z= 0.301 Chirality : 0.043 0.167 5306 Planarity : 0.004 0.060 6138 Dihedral : 8.170 126.574 4933 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 1.49 % Allowed : 15.33 % Favored : 83.18 % 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: 1.13 (0.14), residues: 4274 helix: 1.76 (0.12), residues: 2005 sheet: -0.13 (0.23), residues: 546 loop : -0.07 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.005 0.001 HIS G 290 PHE 0.019 0.001 PHE F 758 TYR 0.028 0.001 TYR G 507 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 1608) hydrogen bonds : angle 4.28305 ( 4524) metal coordination : bond 0.01754 ( 8) metal coordination : angle 2.51037 ( 6) covalent geometry : bond 0.00365 (34819) covalent geometry : angle 0.63091 (47111) Misc. bond : bond 0.00046 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12421.96 seconds wall clock time: 223 minutes 30.93 seconds (13410.93 seconds total)