Starting phenix.real_space_refine on Thu Jun 26 04:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.map" model { file = "/net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dar_27273/06_2025/8dar_27273.cif" } resolution = 3.0 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= -0.029 sd= 1.015 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 30 5.49 5 S 144 5.16 5 C 18857 2.51 5 N 5254 2.21 5 O 5870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30157 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4294 Classifications: {'peptide': 553} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Chain: "B" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4298 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4248 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 3 Chain: "D" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4300 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 524} Chain breaks: 4 Chain: "E" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4166 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 2 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4251 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 4 Chain: "G" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3815 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "H" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 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: 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: "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 25810 SG CYS G 137 42.448 45.406 95.749 1.00 47.25 S ATOM 25870 SG CYS G 145 46.040 46.333 95.040 1.00 40.29 S ATOM 25897 SG CYS G 148 44.681 46.030 98.508 1.00 38.91 S ATOM 26367 SG CYS G 204 72.459 88.210 114.209 1.00 51.99 S ATOM 26465 SG CYS G 216 72.400 89.333 110.696 1.00 38.69 S ATOM 26486 SG CYS G 219 69.772 90.456 112.988 1.00 37.73 S Time building chain proxies: 17.57, per 1000 atoms: 0.58 Number of scatterers: 30157 At special positions: 0 Unit cell: (145.768, 146.832, 172.368, 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 144 16.00 P 30 15.00 O 5870 8.00 N 5254 7.00 C 18857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7148 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 17 sheets defined 57.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.638A pdb=" N ILE A 216 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.545A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.450A 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 238 through 244 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.170A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 329 through 344 removed outlier: 4.200A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.108A pdb=" N ILE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.539A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.355A 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 516 removed outlier: 3.880A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.545A 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 592 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.521A pdb=" N ARG A 645 " --> pdb=" O ALA A 642 " (cutoff:3.500A) 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 719 removed outlier: 3.714A pdb=" N HIS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.723A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 removed outlier: 4.211A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.776A pdb=" N LYS B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 290 through 306 removed outlier: 3.860A pdb=" N SER B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.250A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.635A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.792A pdb=" N ILE B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) 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 413 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 454 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: 4.505A 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: 3.897A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.546A pdb=" N VAL B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.604A pdb=" N ILE B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 719 Processing helix chain 'B' and resid 754 through 764 removed outlier: 3.511A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 788 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.566A pdb=" N LYS C 75 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.647A pdb=" N VAL C 211 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 219 through 236 removed outlier: 4.278A pdb=" N LEU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.572A pdb=" N THR C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 322 through 327' Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.805A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.716A pdb=" N ILE C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 413 Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.721A pdb=" N GLU C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.840A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.683A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.500A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 609 through 621 Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.610A pdb=" N ARG C 645 " --> pdb=" O ALA C 642 " (cutoff:3.500A) 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 719 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.904A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 788 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.660A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.143A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 244 Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.790A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 328 through 344 removed outlier: 3.937A pdb=" N ARG D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.876A pdb=" N ILE D 363 " --> pdb=" O PRO D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 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 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.337A 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 removed outlier: 3.636A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.686A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 568 through 579 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 635 through 639 Processing helix chain 'D' and resid 640 through 645 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 719 Processing helix chain 'D' and resid 754 through 764 removed outlier: 3.800A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 789 Processing helix chain 'E' and resid 212 through 216 removed outlier: 3.663A pdb=" N ILE E 216 " --> pdb=" O TYR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 236 removed outlier: 4.257A 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 236 through 244 removed outlier: 4.487A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 290 through 306 removed outlier: 3.812A pdb=" N SER E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 329 through 344 removed outlier: 4.177A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 454 removed outlier: 3.521A pdb=" N SER E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 472 through 476 removed outlier: 3.692A pdb=" N GLU E 476 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.220A 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 517 removed outlier: 3.809A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.634A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 592 removed outlier: 3.716A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 621 Processing helix chain 'E' and resid 635 through 639 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 Processing helix chain 'E' and resid 682 through 689 Processing helix chain 'E' and resid 693 through 719 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.545A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 Processing helix chain 'F' and resid 212 through 216 removed outlier: 3.608A pdb=" N ILE F 216 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 236 removed outlier: 4.405A 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 237 through 244 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 328 through 344 Processing helix chain 'F' and resid 364 through 368 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 437 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 472 through 476 removed outlier: 3.549A pdb=" N GLU F 476 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.237A 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: 3.863A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 635 through 639 Processing helix chain 'F' and resid 640 through 645 removed outlier: 3.970A 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 719 Processing helix chain 'F' and resid 754 through 763 Processing helix chain 'F' and resid 770 through 787 Processing helix chain 'G' and resid 116 through 125 removed outlier: 3.574A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.851A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 Processing helix chain 'G' and resid 242 through 256 removed outlier: 3.629A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.987A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 402 through 410 removed outlier: 3.908A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 516 through 525 Processing helix chain 'G' and resid 526 through 537 Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 556 through 566 Processing helix chain 'G' and resid 566 through 579 Processing helix chain 'H' and resid 243 through 253 Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.444A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.303A pdb=" N GLN A 651 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.228A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 276 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.645A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY B 523 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILE B 653 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 525 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.198A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.198A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 550 through 552 removed outlier: 6.627A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY C 523 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE C 653 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.908A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 251 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR D 357 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET D 253 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 548 through 552 removed outlier: 6.788A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY D 523 " --> pdb=" O GLN D 651 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 312 through 313 removed outlier: 3.506A pdb=" N ALA E 356 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 548 through 552 removed outlier: 6.529A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.650A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL F 251 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR F 357 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET F 253 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY F 250 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL F 377 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 550 through 552 removed outlier: 6.658A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.052A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 451 " --> pdb=" O TYR G 439 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 463 through 465 removed outlier: 9.993A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET G 263 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU G 324 " --> pdb=" O GLY G 261 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 261 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS G 236 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL G 281 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU G 238 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA G 283 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AB8, first strand: chain 'G' and resid 415 through 416 removed outlier: 3.588A pdb=" N SER G 415 " --> pdb=" O TYR G 424 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4101 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: 10.76 Time building geometry restraints manager: 8.46 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: 10188 1.34 - 1.46: 4786 1.46 - 1.58: 15387 1.58 - 1.69: 48 1.69 - 1.81: 268 Bond restraints: 30677 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 30672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 41101 2.59 - 5.18: 301 5.18 - 7.77: 69 7.77 - 10.36: 19 10.36 - 12.95: 3 Bond angle restraints: 41493 Sorted by residual: angle pdb=" C1' ADP A 902 " pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " ideal model delta sigma weight residual 111.00 98.05 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C1' ADP E 902 " pdb=" C2' ADP E 902 " pdb=" C3' ADP E 902 " ideal model delta sigma weight residual 111.00 98.75 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C1' ADP B 902 " pdb=" C2' ADP B 902 " pdb=" C3' ADP B 902 " ideal model delta sigma weight residual 111.00 99.60 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C1' ADP D 902 " pdb=" C2' ADP D 902 " pdb=" C3' ADP D 902 " ideal model delta sigma weight residual 111.00 100.69 10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.09 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 41488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 18737 35.31 - 70.61: 243 70.61 - 105.92: 8 105.92 - 141.23: 16 141.23 - 176.53: 4 Dihedral angle restraints: 19008 sinusoidal: 7963 harmonic: 11045 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 116.54 -176.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 148.77 151.23 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 88.57 -148.57 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 19005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4195 0.070 - 0.140: 411 0.140 - 0.210: 5 0.210 - 0.280: 9 0.280 - 0.349: 12 Chirality restraints: 4632 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ATP D 901 " pdb=" C2' ATP D 901 " pdb=" C4' ATP D 901 " pdb=" O3' ATP D 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP F 901 " pdb=" C1' ATP F 901 " pdb=" C3' ATP F 901 " pdb=" O2' ATP F 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4629 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO E 506 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 505 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO B 506 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 506 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 506 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 505 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 506 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.019 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 315 2.59 - 3.17: 26913 3.17 - 3.74: 45704 3.74 - 4.32: 62157 4.32 - 4.90: 107011 Nonbonded interactions: 242100 Sorted by model distance: nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 2.011 3.040 nonbonded pdb=" OG SER G 417 " pdb=" O MET G 422 " model vdw 2.059 3.040 nonbonded pdb=" OG SER B 294 " pdb=" OE1 GLU G 436 " model vdw 2.078 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 2.090 3.040 nonbonded pdb=" OG1 THR A 485 " pdb=" OD1 ASP A 487 " model vdw 2.117 3.040 ... (remaining 242095 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 208 through 787 or resid 901 through 902)) selection = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'C' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and (resid 208 through 787 or resid 901 through 902)) selection = chain 'E' selection = (chain 'F' and (resid 208 through 787 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 70.010 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.120 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 30685 Z= 0.186 Angle : 0.598 12.947 41499 Z= 0.276 Chirality : 0.045 0.349 4632 Planarity : 0.003 0.042 5398 Dihedral : 12.519 176.532 11860 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 5.23 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.67 (0.14), residues: 3767 helix: 2.04 (0.12), residues: 1910 sheet: -0.31 (0.24), residues: 458 loop : 0.44 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 486 HIS 0.004 0.001 HIS G 528 PHE 0.011 0.001 PHE G 527 TYR 0.012 0.001 TYR G 172 ARG 0.003 0.000 ARG A 788 Details of bonding type rmsd hydrogen bonds : bond 0.14926 ( 1458) hydrogen bonds : angle 5.17408 ( 4101) metal coordination : bond 0.07600 ( 8) metal coordination : angle 2.66256 ( 6) covalent geometry : bond 0.00395 (30677) covalent geometry : angle 0.59752 (41493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 521 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6711 (mtm110) REVERT: B 209 ASN cc_start: 0.7312 (t0) cc_final: 0.6925 (t0) REVERT: C 571 ASP cc_start: 0.8101 (t0) cc_final: 0.7852 (t0) REVERT: D 785 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8116 (tppt) REVERT: E 331 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 709 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8681 (tp) REVERT: G 257 MET cc_start: 0.7102 (mmp) cc_final: 0.6844 (mmm) outliers start: 62 outliers final: 14 residues processed: 568 average time/residue: 1.8101 time to fit residues: 1169.5474 Evaluate side-chains 283 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 268 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 114 optimal weight: 0.0000 chunk 180 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 343 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A 716 HIS B 432 GLN B 651 GLN C 512 GLN C 638 GLN C 651 GLN C 716 HIS D 306 ASN D 783 GLN E 361 ASN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN F 470 ASN F 668 ASN G 309 GLN G 361 HIS G 537 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.124225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090026 restraints weight = 46703.543| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.86 r_work: 0.3092 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30685 Z= 0.139 Angle : 0.624 14.061 41499 Z= 0.302 Chirality : 0.043 0.204 4632 Planarity : 0.004 0.054 5398 Dihedral : 11.222 170.011 4434 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.87 % Allowed : 12.24 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.65 (0.14), residues: 3767 helix: 1.91 (0.12), residues: 1935 sheet: 0.06 (0.24), residues: 438 loop : 0.40 (0.18), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 561 HIS 0.010 0.001 HIS A 716 PHE 0.021 0.001 PHE B 464 TYR 0.019 0.001 TYR F 416 ARG 0.008 0.000 ARG B 775 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 1458) hydrogen bonds : angle 4.19396 ( 4101) metal coordination : bond 0.00736 ( 8) metal coordination : angle 2.61491 ( 6) covalent geometry : bond 0.00324 (30677) covalent geometry : angle 0.62345 (41493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 304 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7496 (mtp) REVERT: A 480 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: A 609 ARG cc_start: 0.6893 (mtp-110) cc_final: 0.6098 (mtm110) REVERT: B 332 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6845 (mpp-170) REVERT: B 345 MET cc_start: 0.7526 (ttp) cc_final: 0.7295 (ttm) REVERT: B 359 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (ttm110) REVERT: B 553 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8152 (mmtm) REVERT: B 556 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: B 571 ASP cc_start: 0.8396 (t0) cc_final: 0.8186 (t0) REVERT: B 635 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6833 (mmm-85) REVERT: B 763 LYS cc_start: 0.8668 (mttt) cc_final: 0.8113 (mmpt) REVERT: C 437 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7251 (ttp) REVERT: C 571 ASP cc_start: 0.8556 (t0) cc_final: 0.8192 (t0) REVERT: D 304 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: D 398 MET cc_start: 0.8817 (mtp) cc_final: 0.8391 (ttm) REVERT: D 758 PHE cc_start: 0.8585 (m-80) cc_final: 0.8293 (m-80) REVERT: D 762 MET cc_start: 0.7953 (mmm) cc_final: 0.7710 (mmm) REVERT: D 785 LYS cc_start: 0.8271 (tmmt) cc_final: 0.7861 (tppt) REVERT: E 229 MET cc_start: 0.7716 (tpt) cc_final: 0.7162 (tpt) REVERT: E 331 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7787 (mp0) REVERT: E 375 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6783 (mtm110) REVERT: E 438 ASP cc_start: 0.7636 (m-30) cc_final: 0.7245 (p0) REVERT: E 439 LEU cc_start: 0.8446 (tm) cc_final: 0.7884 (pp) REVERT: E 451 VAL cc_start: 0.6481 (t) cc_final: 0.5872 (p) REVERT: E 468 ASN cc_start: 0.7478 (m-40) cc_final: 0.7264 (t0) REVERT: F 278 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8596 (tm) REVERT: F 784 MET cc_start: 0.8210 (tpp) cc_final: 0.7713 (tpp) REVERT: G 206 ASN cc_start: 0.6321 (t0) cc_final: 0.5963 (t0) REVERT: G 257 MET cc_start: 0.8331 (mmp) cc_final: 0.7910 (mmm) REVERT: G 406 GLU cc_start: 0.8057 (tt0) cc_final: 0.7777 (tt0) REVERT: G 495 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7057 (mtp) REVERT: G 537 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7775 (tm-30) outliers start: 92 outliers final: 26 residues processed: 362 average time/residue: 2.0416 time to fit residues: 865.0238 Evaluate side-chains 298 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 309 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 82 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 363 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 327 optimal weight: 0.1980 chunk 246 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 568 ASN C 512 GLN C 568 ASN C 716 HIS ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.091766 restraints weight = 47338.717| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.77 r_work: 0.3075 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30685 Z= 0.123 Angle : 0.570 12.613 41499 Z= 0.275 Chirality : 0.042 0.163 4632 Planarity : 0.004 0.047 5398 Dihedral : 10.526 154.857 4422 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.99 % Allowed : 13.02 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.61 (0.14), residues: 3767 helix: 1.88 (0.12), residues: 1937 sheet: 0.11 (0.24), residues: 446 loop : 0.36 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 561 HIS 0.008 0.001 HIS A 716 PHE 0.017 0.001 PHE B 464 TYR 0.017 0.001 TYR G 189 ARG 0.004 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1458) hydrogen bonds : angle 3.96017 ( 4101) metal coordination : bond 0.00666 ( 8) metal coordination : angle 2.00903 ( 6) covalent geometry : bond 0.00291 (30677) covalent geometry : angle 0.56974 (41493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 273 time to evaluate : 5.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: A 480 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: A 497 GLU cc_start: 0.8015 (mp0) cc_final: 0.7780 (mp0) REVERT: A 556 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: A 609 ARG cc_start: 0.7090 (mtp-110) cc_final: 0.6264 (mtm110) REVERT: A 621 MET cc_start: 0.8081 (ttm) cc_final: 0.7573 (ttp) REVERT: B 345 MET cc_start: 0.7815 (ttp) cc_final: 0.7547 (ttm) REVERT: B 359 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8114 (ttm110) REVERT: B 375 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7349 (mmt90) REVERT: B 476 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: B 553 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8255 (mmtm) REVERT: B 556 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 571 ASP cc_start: 0.8631 (t0) cc_final: 0.8388 (t0) REVERT: B 635 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6900 (mmm-85) REVERT: B 672 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7347 (ptp90) REVERT: B 763 LYS cc_start: 0.8705 (mttt) cc_final: 0.8136 (mmpt) REVERT: C 376 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: C 437 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7295 (ttp) REVERT: C 571 ASP cc_start: 0.8662 (t0) cc_final: 0.8305 (t0) REVERT: C 665 SER cc_start: 0.9030 (t) cc_final: 0.8738 (p) REVERT: D 264 MET cc_start: 0.8693 (mtp) cc_final: 0.8443 (mtp) REVERT: D 304 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: D 398 MET cc_start: 0.8904 (mtp) cc_final: 0.8402 (ttm) REVERT: D 758 PHE cc_start: 0.8747 (m-80) cc_final: 0.8488 (m-80) REVERT: D 762 MET cc_start: 0.8037 (mmm) cc_final: 0.7791 (mmm) REVERT: D 785 LYS cc_start: 0.8345 (tmmt) cc_final: 0.7903 (tppt) REVERT: E 229 MET cc_start: 0.7799 (tpt) cc_final: 0.6154 (tpt) REVERT: E 302 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7998 (mp0) REVERT: E 331 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7784 (mp0) REVERT: E 375 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.5926 (mtp85) REVERT: E 635 ARG cc_start: 0.7291 (mtp85) cc_final: 0.6966 (mtp85) REVERT: E 673 LYS cc_start: 0.8603 (pptt) cc_final: 0.8120 (tmmm) REVERT: F 278 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8681 (tm) REVERT: F 298 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8136 (mmmt) REVERT: F 342 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7935 (mmt) REVERT: G 122 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7640 (mm) REVERT: G 146 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7433 (tt0) REVERT: G 206 ASN cc_start: 0.6674 (t0) cc_final: 0.6236 (t0) REVERT: G 406 GLU cc_start: 0.8069 (tt0) cc_final: 0.7794 (tt0) REVERT: G 495 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7040 (mtp) REVERT: G 537 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7725 (tm-30) REVERT: H 237 SER cc_start: 0.8452 (m) cc_final: 0.8170 (t) outliers start: 96 outliers final: 30 residues processed: 343 average time/residue: 2.0253 time to fit residues: 807.5280 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 363 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 368 optimal weight: 0.7980 chunk 348 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 361 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 568 ASN C 512 GLN D 361 ASN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091754 restraints weight = 47545.519| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.73 r_work: 0.3079 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30685 Z= 0.121 Angle : 0.554 11.856 41499 Z= 0.267 Chirality : 0.041 0.164 4632 Planarity : 0.004 0.048 5398 Dihedral : 10.099 146.737 4422 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.93 % Allowed : 13.64 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.61 (0.14), residues: 3767 helix: 1.89 (0.12), residues: 1937 sheet: 0.17 (0.24), residues: 451 loop : 0.32 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 561 HIS 0.005 0.001 HIS A 716 PHE 0.014 0.001 PHE B 464 TYR 0.014 0.001 TYR A 416 ARG 0.003 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1458) hydrogen bonds : angle 3.85532 ( 4101) metal coordination : bond 0.00545 ( 8) metal coordination : angle 1.93250 ( 6) covalent geometry : bond 0.00287 (30677) covalent geometry : angle 0.55329 (41493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7552 (mtp) REVERT: A 480 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: A 497 GLU cc_start: 0.8029 (mp0) cc_final: 0.7772 (mp0) REVERT: A 556 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 621 MET cc_start: 0.8115 (ttm) cc_final: 0.7620 (ttp) REVERT: B 345 MET cc_start: 0.7732 (ttp) cc_final: 0.7198 (ttp) REVERT: B 359 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (ttm110) REVERT: B 375 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7415 (mmt90) REVERT: B 476 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: B 497 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: B 553 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8223 (mmtm) REVERT: B 556 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 560 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7223 (mtt) REVERT: B 571 ASP cc_start: 0.8672 (t0) cc_final: 0.8425 (t0) REVERT: B 635 ARG cc_start: 0.7492 (mmm160) cc_final: 0.6878 (mmm-85) REVERT: B 763 LYS cc_start: 0.8702 (mttt) cc_final: 0.8131 (mmpt) REVERT: C 376 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: C 437 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7314 (ttp) REVERT: C 571 ASP cc_start: 0.8679 (t0) cc_final: 0.8324 (t0) REVERT: C 614 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 618 MET cc_start: 0.8597 (mtp) cc_final: 0.8296 (mtm) REVERT: C 665 SER cc_start: 0.9030 (t) cc_final: 0.8742 (p) REVERT: C 755 LYS cc_start: 0.6833 (tttt) cc_final: 0.6508 (tptp) REVERT: D 264 MET cc_start: 0.8729 (mtp) cc_final: 0.8441 (mtp) REVERT: D 304 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: D 361 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8333 (p0) REVERT: D 468 ASN cc_start: 0.7110 (t0) cc_final: 0.6908 (t0) REVERT: D 758 PHE cc_start: 0.8803 (m-80) cc_final: 0.8594 (m-80) REVERT: D 762 MET cc_start: 0.8110 (mmm) cc_final: 0.7877 (mmm) REVERT: D 785 LYS cc_start: 0.8372 (tmmt) cc_final: 0.7889 (tppt) REVERT: E 331 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7780 (mp0) REVERT: E 448 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6962 (p0) REVERT: E 635 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7023 (mtp85) REVERT: F 253 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: F 298 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8170 (mmmt) REVERT: F 427 GLU cc_start: 0.7825 (tt0) cc_final: 0.7378 (tt0) REVERT: F 571 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: F 784 MET cc_start: 0.8248 (tpp) cc_final: 0.7729 (tpp) REVERT: G 206 ASN cc_start: 0.6703 (t0) cc_final: 0.6257 (t0) REVERT: G 371 TYR cc_start: 0.8843 (m-80) cc_final: 0.8463 (m-80) REVERT: G 406 GLU cc_start: 0.8172 (tt0) cc_final: 0.7916 (tt0) REVERT: G 422 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8030 (mtp) REVERT: G 495 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7048 (mtp) REVERT: G 537 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7769 (tm-30) REVERT: H 237 SER cc_start: 0.8501 (m) cc_final: 0.8287 (t) outliers start: 94 outliers final: 35 residues processed: 327 average time/residue: 1.5418 time to fit residues: 586.8885 Evaluate side-chains 306 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 52 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 368 optimal weight: 0.6980 chunk 228 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 270 ASN B 568 ASN C 512 GLN D 361 ASN D 470 ASN G 491 ASN G 493 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091203 restraints weight = 47164.621| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.71 r_work: 0.3078 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30685 Z= 0.129 Angle : 0.559 11.055 41499 Z= 0.268 Chirality : 0.042 0.258 4632 Planarity : 0.004 0.049 5398 Dihedral : 9.856 144.952 4420 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.15 % Allowed : 13.98 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.62 (0.14), residues: 3767 helix: 1.91 (0.12), residues: 1933 sheet: 0.24 (0.24), residues: 449 loop : 0.29 (0.18), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.016 0.001 HIS A 716 PHE 0.012 0.001 PHE B 464 TYR 0.013 0.001 TYR G 189 ARG 0.005 0.000 ARG A 717 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1458) hydrogen bonds : angle 3.82042 ( 4101) metal coordination : bond 0.00554 ( 8) metal coordination : angle 1.68236 ( 6) covalent geometry : bond 0.00310 (30677) covalent geometry : angle 0.55845 (41493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 265 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7511 (mtp) REVERT: A 480 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 556 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 561 TRP cc_start: 0.6727 (t-100) cc_final: 0.6321 (t60) REVERT: A 609 ARG cc_start: 0.6943 (mtm110) cc_final: 0.6124 (mtm110) REVERT: A 621 MET cc_start: 0.8116 (ttm) cc_final: 0.7631 (ttp) REVERT: B 345 MET cc_start: 0.7714 (ttp) cc_final: 0.7179 (ttp) REVERT: B 359 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8053 (ttm110) REVERT: B 375 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7397 (mmt90) REVERT: B 476 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: B 497 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: B 553 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8199 (mmtm) REVERT: B 556 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: B 560 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7225 (mtt) REVERT: B 571 ASP cc_start: 0.8701 (t70) cc_final: 0.8433 (t0) REVERT: B 635 ARG cc_start: 0.7509 (mmm160) cc_final: 0.6904 (mmm-85) REVERT: B 763 LYS cc_start: 0.8688 (mttt) cc_final: 0.8125 (mmpt) REVERT: C 376 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: C 437 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7377 (ttp) REVERT: C 568 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7027 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8677 (t0) cc_final: 0.8175 (t0) REVERT: C 614 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8312 (tt) REVERT: C 618 MET cc_start: 0.8525 (mtp) cc_final: 0.8212 (mtm) REVERT: C 665 SER cc_start: 0.9033 (t) cc_final: 0.8744 (p) REVERT: C 755 LYS cc_start: 0.6852 (tttt) cc_final: 0.6520 (tptp) REVERT: D 264 MET cc_start: 0.8731 (mtp) cc_final: 0.8455 (mtp) REVERT: D 304 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 398 MET cc_start: 0.8960 (mtp) cc_final: 0.8518 (ttm) REVERT: D 468 ASN cc_start: 0.7344 (t0) cc_final: 0.7134 (t0) REVERT: D 758 PHE cc_start: 0.8836 (m-80) cc_final: 0.8615 (m-80) REVERT: D 762 MET cc_start: 0.8170 (mmm) cc_final: 0.7947 (mmm) REVERT: D 785 LYS cc_start: 0.8386 (tmmt) cc_final: 0.7895 (tppt) REVERT: E 331 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7778 (mp0) REVERT: E 437 MET cc_start: 0.6784 (ttt) cc_final: 0.6571 (ttp) REVERT: E 448 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6846 (p0) REVERT: E 635 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7037 (mtp85) REVERT: E 762 MET cc_start: 0.7334 (mmm) cc_final: 0.7102 (tpt) REVERT: F 253 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8631 (mtp) REVERT: F 298 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8159 (mmmt) REVERT: F 556 GLU cc_start: 0.7610 (tp30) cc_final: 0.7376 (mt-10) REVERT: F 571 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8300 (t0) REVERT: F 784 MET cc_start: 0.8252 (tpp) cc_final: 0.7772 (tpp) REVERT: G 122 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7676 (mm) REVERT: G 146 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7222 (tt0) REVERT: G 206 ASN cc_start: 0.6685 (t0) cc_final: 0.6243 (t0) REVERT: G 406 GLU cc_start: 0.8159 (tt0) cc_final: 0.7915 (tt0) REVERT: G 422 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: G 495 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: G 537 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 101 outliers final: 38 residues processed: 336 average time/residue: 1.5864 time to fit residues: 617.7341 Evaluate side-chains 306 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 136 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 269 optimal weight: 0.0060 chunk 282 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 568 ASN C 512 GLN D 470 ASN G 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090655 restraints weight = 47262.012| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.92 r_work: 0.3071 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30685 Z= 0.119 Angle : 0.556 13.448 41499 Z= 0.265 Chirality : 0.041 0.222 4632 Planarity : 0.004 0.049 5398 Dihedral : 9.632 146.472 4420 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.77 % Allowed : 14.54 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.62 (0.14), residues: 3767 helix: 1.92 (0.12), residues: 1935 sheet: 0.29 (0.24), residues: 447 loop : 0.25 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.011 0.001 HIS A 716 PHE 0.011 0.001 PHE B 464 TYR 0.013 0.001 TYR G 189 ARG 0.004 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1458) hydrogen bonds : angle 3.77359 ( 4101) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.72740 ( 6) covalent geometry : bond 0.00281 (30677) covalent geometry : angle 0.55535 (41493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 256 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7551 (mtp) REVERT: A 480 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: A 556 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: A 561 TRP cc_start: 0.6801 (t-100) cc_final: 0.6359 (t60) REVERT: A 609 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6159 (mtm110) REVERT: A 618 MET cc_start: 0.8344 (mtp) cc_final: 0.8122 (mtp) REVERT: A 621 MET cc_start: 0.8116 (ttm) cc_final: 0.7623 (ttp) REVERT: B 345 MET cc_start: 0.7843 (ttp) cc_final: 0.7305 (ttp) REVERT: B 359 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8077 (ttm110) REVERT: B 375 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7394 (mmt90) REVERT: B 553 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8194 (mmtm) REVERT: B 556 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: B 560 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7398 (mtt) REVERT: B 571 ASP cc_start: 0.8739 (t70) cc_final: 0.8489 (t0) REVERT: B 635 ARG cc_start: 0.7517 (mmm160) cc_final: 0.6906 (mmm-85) REVERT: B 763 LYS cc_start: 0.8690 (mttt) cc_final: 0.8125 (mmpt) REVERT: C 376 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: C 568 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7244 (p0) REVERT: C 571 ASP cc_start: 0.8690 (t0) cc_final: 0.8215 (t0) REVERT: C 614 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 618 MET cc_start: 0.8562 (mtp) cc_final: 0.8246 (mtm) REVERT: C 665 SER cc_start: 0.9043 (t) cc_final: 0.8759 (p) REVERT: C 755 LYS cc_start: 0.6931 (tttt) cc_final: 0.6599 (tptp) REVERT: D 264 MET cc_start: 0.8770 (mtp) cc_final: 0.8457 (mtp) REVERT: D 304 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: D 361 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8568 (p0) REVERT: D 398 MET cc_start: 0.8953 (mtp) cc_final: 0.8495 (ttm) REVERT: D 412 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: D 556 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7245 (mt-10) REVERT: D 758 PHE cc_start: 0.8767 (m-80) cc_final: 0.8535 (m-80) REVERT: D 762 MET cc_start: 0.8153 (mmm) cc_final: 0.7924 (mmm) REVERT: D 785 LYS cc_start: 0.8443 (tmmt) cc_final: 0.7948 (tppt) REVERT: E 229 MET cc_start: 0.7423 (tpp) cc_final: 0.7128 (tpt) REVERT: E 331 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 437 MET cc_start: 0.6696 (ttt) cc_final: 0.6478 (ttp) REVERT: E 635 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7047 (mtp85) REVERT: F 298 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8178 (mmmt) REVERT: F 556 GLU cc_start: 0.7606 (tp30) cc_final: 0.7392 (tp30) REVERT: F 784 MET cc_start: 0.8190 (tpp) cc_final: 0.7743 (tpp) REVERT: G 122 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7686 (mm) REVERT: G 206 ASN cc_start: 0.6708 (t0) cc_final: 0.6221 (t0) REVERT: G 406 GLU cc_start: 0.8190 (tt0) cc_final: 0.7958 (tt0) REVERT: G 495 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7075 (mtp) REVERT: G 537 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7821 (tm-30) outliers start: 89 outliers final: 37 residues processed: 317 average time/residue: 1.7156 time to fit residues: 633.3403 Evaluate side-chains 301 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 210 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 299 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS A 716 HIS B 568 ASN C 512 GLN D 394 HIS D 470 ASN D 509 HIS F 470 ASN G 362 GLN G 491 ASN G 493 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089032 restraints weight = 47507.066| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.79 r_work: 0.3041 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30685 Z= 0.195 Angle : 0.600 12.815 41499 Z= 0.291 Chirality : 0.044 0.200 4632 Planarity : 0.004 0.062 5398 Dihedral : 9.674 148.521 4420 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.96 % Allowed : 14.67 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.50 (0.14), residues: 3767 helix: 1.81 (0.12), residues: 1928 sheet: 0.21 (0.24), residues: 453 loop : 0.21 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 561 HIS 0.007 0.001 HIS A 716 PHE 0.016 0.002 PHE D 276 TYR 0.016 0.001 TYR F 416 ARG 0.014 0.000 ARG E 375 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 1458) hydrogen bonds : angle 3.88242 ( 4101) metal coordination : bond 0.00855 ( 8) metal coordination : angle 1.76668 ( 6) covalent geometry : bond 0.00479 (30677) covalent geometry : angle 0.60009 (41493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 252 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7523 (mtp) REVERT: A 480 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: A 556 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: A 561 TRP cc_start: 0.6807 (t-100) cc_final: 0.6316 (t60) REVERT: A 609 ARG cc_start: 0.6984 (mtm110) cc_final: 0.6236 (mtm110) REVERT: A 621 MET cc_start: 0.8184 (ttm) cc_final: 0.7845 (ttp) REVERT: B 345 MET cc_start: 0.7989 (ttp) cc_final: 0.7788 (ttp) REVERT: B 359 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (ttm110) REVERT: B 375 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7414 (mmt90) REVERT: B 553 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8206 (mmtm) REVERT: B 556 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: B 624 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8273 (mtpm) REVERT: B 635 ARG cc_start: 0.7487 (mmm160) cc_final: 0.6814 (mmm-85) REVERT: B 763 LYS cc_start: 0.8682 (mttt) cc_final: 0.8140 (mmpt) REVERT: C 376 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: C 568 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7381 (p0) REVERT: C 571 ASP cc_start: 0.8732 (t0) cc_final: 0.8249 (t0) REVERT: C 614 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8261 (tt) REVERT: C 618 MET cc_start: 0.8581 (mtp) cc_final: 0.8250 (mtm) REVERT: C 665 SER cc_start: 0.9058 (t) cc_final: 0.8766 (p) REVERT: C 755 LYS cc_start: 0.7020 (tttt) cc_final: 0.6634 (tptp) REVERT: D 264 MET cc_start: 0.8748 (mtp) cc_final: 0.8404 (mtp) REVERT: D 304 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: D 412 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: D 556 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 762 MET cc_start: 0.8200 (mmm) cc_final: 0.7967 (mmm) REVERT: D 785 LYS cc_start: 0.8411 (tmmt) cc_final: 0.7938 (tppt) REVERT: E 331 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 437 MET cc_start: 0.6781 (ttt) cc_final: 0.6557 (ttp) REVERT: E 566 GLU cc_start: 0.7165 (pm20) cc_final: 0.6916 (pm20) REVERT: E 635 ARG cc_start: 0.7337 (mtp85) cc_final: 0.7099 (mtp85) REVERT: F 298 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8154 (mmmt) REVERT: F 556 GLU cc_start: 0.7616 (tp30) cc_final: 0.7332 (tp30) REVERT: F 571 ASP cc_start: 0.8763 (t0) cc_final: 0.8312 (m-30) REVERT: F 784 MET cc_start: 0.8198 (tpp) cc_final: 0.7713 (tpp) REVERT: G 122 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7648 (mm) REVERT: G 146 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7191 (tt0) REVERT: G 206 ASN cc_start: 0.6750 (t0) cc_final: 0.6326 (t0) REVERT: G 289 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.6215 (pp30) REVERT: G 406 GLU cc_start: 0.8174 (tt0) cc_final: 0.7937 (tt0) REVERT: G 495 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7110 (mtp) REVERT: G 537 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7816 (tm-30) outliers start: 95 outliers final: 38 residues processed: 329 average time/residue: 1.5628 time to fit residues: 595.6676 Evaluate side-chains 301 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 522 GLU Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 158 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 377 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 350 optimal weight: 0.7980 chunk 359 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 568 ASN C 512 GLN D 470 ASN D 719 HIS G 362 GLN G 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090299 restraints weight = 47256.338| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.83 r_work: 0.3065 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30685 Z= 0.126 Angle : 0.575 11.996 41499 Z= 0.275 Chirality : 0.042 0.201 4632 Planarity : 0.004 0.054 5398 Dihedral : 9.410 147.933 4420 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.24 % Allowed : 15.70 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.54 (0.14), residues: 3767 helix: 1.85 (0.12), residues: 1931 sheet: 0.26 (0.24), residues: 445 loop : 0.22 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 561 HIS 0.011 0.001 HIS A 716 PHE 0.012 0.001 PHE F 573 TYR 0.012 0.001 TYR F 416 ARG 0.013 0.000 ARG E 375 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 1458) hydrogen bonds : angle 3.81179 ( 4101) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.58080 ( 6) covalent geometry : bond 0.00299 (30677) covalent geometry : angle 0.57425 (41493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7531 (mtp) REVERT: A 556 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: A 561 TRP cc_start: 0.6816 (t-100) cc_final: 0.6298 (t60) REVERT: A 621 MET cc_start: 0.8166 (ttm) cc_final: 0.7759 (ttp) REVERT: B 345 MET cc_start: 0.8014 (ttp) cc_final: 0.7812 (ttp) REVERT: B 359 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8099 (ttm110) REVERT: B 375 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7407 (mmt90) REVERT: B 553 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8272 (mmtm) REVERT: B 556 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: B 568 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 571 ASP cc_start: 0.8714 (t70) cc_final: 0.8484 (t0) REVERT: B 635 ARG cc_start: 0.7474 (mmm160) cc_final: 0.6817 (mmm-85) REVERT: B 763 LYS cc_start: 0.8687 (mttt) cc_final: 0.8117 (mmpt) REVERT: C 376 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: C 568 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7431 (p0) REVERT: C 571 ASP cc_start: 0.8711 (t0) cc_final: 0.8245 (t0) REVERT: C 614 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 665 SER cc_start: 0.9061 (t) cc_final: 0.8778 (p) REVERT: C 755 LYS cc_start: 0.6995 (tttt) cc_final: 0.6584 (tptp) REVERT: D 264 MET cc_start: 0.8759 (mtp) cc_final: 0.8418 (mtp) REVERT: D 304 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: D 398 MET cc_start: 0.8996 (mtp) cc_final: 0.8642 (ttm) REVERT: D 412 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: D 556 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 709 ILE cc_start: 0.7936 (tt) cc_final: 0.7724 (tt) REVERT: D 762 MET cc_start: 0.8199 (mmm) cc_final: 0.7973 (mmm) REVERT: D 785 LYS cc_start: 0.8434 (tmmt) cc_final: 0.7947 (tppt) REVERT: E 331 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7873 (mt-10) REVERT: E 437 MET cc_start: 0.6702 (ttt) cc_final: 0.6480 (ttp) REVERT: E 566 GLU cc_start: 0.7169 (pm20) cc_final: 0.6915 (pm20) REVERT: E 635 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7099 (mtp85) REVERT: F 298 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8181 (mmmt) REVERT: F 556 GLU cc_start: 0.7636 (tp30) cc_final: 0.7336 (tp30) REVERT: F 571 ASP cc_start: 0.8748 (t0) cc_final: 0.8283 (m-30) REVERT: F 784 MET cc_start: 0.8207 (tpp) cc_final: 0.7786 (tpp) REVERT: G 206 ASN cc_start: 0.6761 (t0) cc_final: 0.6343 (t0) REVERT: G 257 MET cc_start: 0.8228 (mmt) cc_final: 0.8019 (mmm) REVERT: G 406 GLU cc_start: 0.8196 (tt0) cc_final: 0.7967 (tt0) REVERT: G 495 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (mtp) REVERT: G 537 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7838 (tm-30) outliers start: 72 outliers final: 40 residues processed: 313 average time/residue: 1.5950 time to fit residues: 581.7398 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 140 optimal weight: 0.0060 chunk 201 optimal weight: 0.5980 chunk 336 optimal weight: 0.9980 chunk 235 optimal weight: 0.3980 chunk 344 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 568 ASN C 512 GLN D 470 ASN D 719 HIS G 491 ASN G 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090888 restraints weight = 47163.288| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.71 r_work: 0.3085 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30685 Z= 0.106 Angle : 0.569 14.804 41499 Z= 0.270 Chirality : 0.041 0.200 4632 Planarity : 0.004 0.075 5398 Dihedral : 9.169 144.299 4420 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.96 % Allowed : 16.19 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.61 (0.14), residues: 3767 helix: 1.92 (0.12), residues: 1930 sheet: 0.35 (0.24), residues: 442 loop : 0.21 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 561 HIS 0.014 0.001 HIS A 716 PHE 0.010 0.001 PHE C 277 TYR 0.013 0.001 TYR G 189 ARG 0.016 0.000 ARG E 375 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 1458) hydrogen bonds : angle 3.73679 ( 4101) metal coordination : bond 0.00285 ( 8) metal coordination : angle 1.80323 ( 6) covalent geometry : bond 0.00244 (30677) covalent geometry : angle 0.56823 (41493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7490 (mtp) REVERT: A 556 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: A 621 MET cc_start: 0.8125 (ttm) cc_final: 0.7706 (ttp) REVERT: B 243 ILE cc_start: 0.7960 (tt) cc_final: 0.7758 (tt) REVERT: B 375 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7365 (mmt90) REVERT: B 553 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8177 (mmtm) REVERT: B 556 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: B 568 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 635 ARG cc_start: 0.7444 (mmm160) cc_final: 0.6856 (mmm-85) REVERT: B 763 LYS cc_start: 0.8673 (mttt) cc_final: 0.8101 (mmpt) REVERT: C 376 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: C 568 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7355 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8669 (t0) cc_final: 0.8181 (t0) REVERT: C 614 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8232 (tt) REVERT: C 618 MET cc_start: 0.8568 (mtp) cc_final: 0.8345 (mtm) REVERT: C 665 SER cc_start: 0.9024 (t) cc_final: 0.8743 (p) REVERT: C 755 LYS cc_start: 0.6955 (tttt) cc_final: 0.6546 (tptp) REVERT: D 264 MET cc_start: 0.8697 (mtp) cc_final: 0.8365 (mtp) REVERT: D 304 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: D 398 MET cc_start: 0.8941 (mtp) cc_final: 0.8602 (ttm) REVERT: D 412 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: D 556 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7624 (mm-30) REVERT: D 709 ILE cc_start: 0.7881 (tt) cc_final: 0.7674 (tt) REVERT: D 762 MET cc_start: 0.8193 (mmm) cc_final: 0.7973 (mmm) REVERT: D 785 LYS cc_start: 0.8454 (tmmt) cc_final: 0.7988 (tppt) REVERT: E 331 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7849 (mt-10) REVERT: E 437 MET cc_start: 0.6659 (ttt) cc_final: 0.6434 (ttp) REVERT: E 566 GLU cc_start: 0.7156 (pm20) cc_final: 0.6900 (pm20) REVERT: E 635 ARG cc_start: 0.7286 (mtp85) cc_final: 0.7010 (mtp85) REVERT: F 264 MET cc_start: 0.8548 (mtt) cc_final: 0.8034 (mtt) REVERT: F 298 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8096 (mmmt) REVERT: F 556 GLU cc_start: 0.7628 (tp30) cc_final: 0.7333 (tp30) REVERT: F 571 ASP cc_start: 0.8706 (t0) cc_final: 0.8240 (m-30) REVERT: F 784 MET cc_start: 0.8173 (tpp) cc_final: 0.7901 (tpp) REVERT: G 122 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7882 (mt) REVERT: G 146 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6970 (tt0) REVERT: G 206 ASN cc_start: 0.6620 (t0) cc_final: 0.6145 (t0) REVERT: G 289 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: G 406 GLU cc_start: 0.8107 (tt0) cc_final: 0.7886 (tt0) REVERT: G 495 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7147 (mtp) REVERT: G 537 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7831 (tm-30) outliers start: 63 outliers final: 30 residues processed: 300 average time/residue: 1.5773 time to fit residues: 549.5609 Evaluate side-chains 287 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 316 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 372 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 338 optimal weight: 0.4980 chunk 8 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS C 512 GLN D 470 ASN D 719 HIS F 668 ASN G 491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.124327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091139 restraints weight = 47361.794| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.69 r_work: 0.3100 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 30685 Z= 0.107 Angle : 0.575 11.941 41499 Z= 0.273 Chirality : 0.041 0.237 4632 Planarity : 0.004 0.051 5398 Dihedral : 8.901 140.282 4413 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.81 % Allowed : 16.63 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.66 (0.14), residues: 3767 helix: 1.96 (0.12), residues: 1931 sheet: 0.36 (0.24), residues: 448 loop : 0.23 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 561 HIS 0.009 0.001 HIS A 716 PHE 0.013 0.001 PHE D 276 TYR 0.013 0.001 TYR G 189 ARG 0.013 0.000 ARG E 375 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 1458) hydrogen bonds : angle 3.70741 ( 4101) metal coordination : bond 0.00298 ( 8) metal coordination : angle 1.56391 ( 6) covalent geometry : bond 0.00249 (30677) covalent geometry : angle 0.57493 (41493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7474 (mtp) REVERT: A 556 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: A 618 MET cc_start: 0.8312 (mtp) cc_final: 0.8098 (mtp) REVERT: A 621 MET cc_start: 0.8118 (ttm) cc_final: 0.7636 (ttp) REVERT: B 375 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7356 (mmt90) REVERT: B 553 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8217 (mmtm) REVERT: B 556 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: B 568 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 635 ARG cc_start: 0.7520 (mmm160) cc_final: 0.6893 (mmm-85) REVERT: B 763 LYS cc_start: 0.8659 (mttt) cc_final: 0.8084 (mmpt) REVERT: C 376 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: C 568 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7420 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8677 (t0) cc_final: 0.8220 (t0) REVERT: C 614 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8296 (tt) REVERT: C 618 MET cc_start: 0.8586 (mtp) cc_final: 0.8354 (mtm) REVERT: C 665 SER cc_start: 0.9060 (t) cc_final: 0.8781 (p) REVERT: C 755 LYS cc_start: 0.6955 (tttt) cc_final: 0.6602 (tptp) REVERT: D 264 MET cc_start: 0.8723 (mtp) cc_final: 0.8394 (mtp) REVERT: D 304 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: D 398 MET cc_start: 0.8970 (mtp) cc_final: 0.8633 (ttm) REVERT: D 412 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: D 556 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 709 ILE cc_start: 0.7934 (tt) cc_final: 0.7720 (tt) REVERT: D 762 MET cc_start: 0.8205 (mmm) cc_final: 0.7974 (mmm) REVERT: D 785 LYS cc_start: 0.8499 (tmmt) cc_final: 0.8004 (tppt) REVERT: E 331 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7838 (mt-10) REVERT: E 396 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8479 (ttmm) REVERT: E 437 MET cc_start: 0.6694 (ttt) cc_final: 0.6468 (ttp) REVERT: E 566 GLU cc_start: 0.7144 (pm20) cc_final: 0.6914 (pm20) REVERT: E 635 ARG cc_start: 0.7363 (mtp85) cc_final: 0.7078 (mtp85) REVERT: F 298 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8100 (mmmt) REVERT: F 556 GLU cc_start: 0.7637 (tp30) cc_final: 0.7346 (tp30) REVERT: F 571 ASP cc_start: 0.8731 (t0) cc_final: 0.8280 (m-30) REVERT: F 784 MET cc_start: 0.8186 (tpp) cc_final: 0.7929 (tpp) REVERT: G 122 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7997 (mt) REVERT: G 146 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6997 (tt0) REVERT: G 206 ASN cc_start: 0.6683 (t0) cc_final: 0.6045 (t0) REVERT: G 289 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: G 406 GLU cc_start: 0.8099 (tt0) cc_final: 0.7880 (tt0) REVERT: G 495 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7148 (mtp) REVERT: G 537 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7785 (tm-30) outliers start: 58 outliers final: 33 residues processed: 296 average time/residue: 2.4514 time to fit residues: 868.8352 Evaluate side-chains 292 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 357 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 298 optimal weight: 3.9990 chunk 114 optimal weight: 0.0000 chunk 147 optimal weight: 0.4980 chunk 358 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS C 512 GLN D 470 ASN D 719 HIS G 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093272 restraints weight = 47138.794| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.75 r_work: 0.3096 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30685 Z= 0.106 Angle : 0.567 11.815 41499 Z= 0.269 Chirality : 0.041 0.195 4632 Planarity : 0.004 0.065 5398 Dihedral : 8.759 136.640 4413 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.78 % Allowed : 16.69 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.73 (0.14), residues: 3767 helix: 2.01 (0.12), residues: 1924 sheet: 0.37 (0.24), residues: 452 loop : 0.30 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 561 HIS 0.034 0.001 HIS A 716 PHE 0.014 0.001 PHE F 373 TYR 0.013 0.001 TYR G 189 ARG 0.014 0.000 ARG E 375 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 1458) hydrogen bonds : angle 3.68062 ( 4101) metal coordination : bond 0.00277 ( 8) metal coordination : angle 1.38809 ( 6) covalent geometry : bond 0.00243 (30677) covalent geometry : angle 0.56633 (41493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20899.24 seconds wall clock time: 368 minutes 49.39 seconds (22129.39 seconds total)