Starting phenix.real_space_refine on Mon Jul 6 09:25:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.cif" model { file = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8das_27274/07_2026/8das_27274.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 sd= 1.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 29 5.49 5 S 156 5.16 5 C 21316 2.51 5 N 5920 2.21 5 O 6636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34059 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5560 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4385 Classifications: {'peptide': 564} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 534} Chain breaks: 5 Chain: "C" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5590 Classifications: {'peptide': 716} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 678} Chain breaks: 2 Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4365 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} Chain breaks: 4 Chain: "E" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4174 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 2 Chain: "F" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4190 Classifications: {'peptide': 541} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 511} Chain breaks: 2 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: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "J" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 581 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} 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 28517 SG CYS G 137 42.490 46.648 95.636 1.00 75.98 S ATOM 28577 SG CYS G 145 46.079 47.436 95.068 1.00 61.42 S ATOM 28604 SG CYS G 148 44.717 46.971 98.444 1.00 62.85 S ATOM 29074 SG CYS G 204 71.751 88.637 114.245 1.00 85.09 S ATOM 29172 SG CYS G 216 72.055 90.528 111.078 1.00 68.03 S ATOM 29193 SG CYS G 219 69.351 91.363 113.359 1.00 67.48 S Time building chain proxies: 6.09, per 1000 atoms: 0.18 Number of scatterers: 34059 At special positions: 0 Unit cell: (146.832, 167.048, 192.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 156 16.00 P 29 15.00 O 6636 8.00 N 5920 7.00 C 21316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.2 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 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8074 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 24 sheets defined 53.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 130 through 134 removed outlier: 4.041A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.086A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.596A pdb=" N GLU A 204 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.508A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.597A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 329 through 346 removed outlier: 4.147A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.054A 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 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 454 Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.546A pdb=" N PHE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.109A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.762A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.746A 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 removed outlier: 3.551A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 719 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.708A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 removed outlier: 4.203A 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: 3.583A 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 280 through 286 removed outlier: 3.506A pdb=" N VAL B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 removed outlier: 4.240A pdb=" N SER B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.588A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 346 " --> pdb=" O MET B 342 " (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 453 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: 4.583A 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: 3.946A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 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 593 removed outlier: 4.372A pdb=" N ILE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 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 765 removed outlier: 3.809A 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 52 through 59 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 139 through 150 removed outlier: 4.130A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix removed outlier: 3.701A pdb=" N VAL C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.896A pdb=" N GLU C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 219 through 236 removed outlier: 4.487A 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 280 through 286 removed outlier: 3.667A pdb=" N VAL C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.819A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (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 removed outlier: 3.519A pdb=" N LEU C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 436 Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.804A 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: 3.745A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.506A 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 588 through 592 Processing helix chain 'C' and resid 609 through 621 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 659 through 671 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 693 through 719 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.681A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 788 Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.651A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.130A 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 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 328 through 346 removed outlier: 4.346A pdb=" N LYS D 346 " --> pdb=" O MET D 342 " (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 453 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.470A 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: 3.876A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.674A 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 609 through 621 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: 3.952A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 787 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 236 removed outlier: 4.119A 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: 4.418A 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 291 through 306 removed outlier: 3.729A pdb=" N ASN E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.589A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.325A 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 448 through 454 Processing helix chain 'E' and resid 458 through 469 removed outlier: 3.509A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 476 Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.270A 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: 3.796A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 609 through 621 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 Processing helix chain 'E' and resid 672 through 674 No H-bonds generated for 'chain 'E' and resid 672 through 674' 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: 3.515A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 removed outlier: 3.513A pdb=" N LEU E 774 " --> pdb=" O SER E 770 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 4.624A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 236 through 244 removed outlier: 4.441A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 290 through 306 removed outlier: 4.146A pdb=" N SER F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 328 through 345 Processing helix chain 'F' and resid 346 through 348 No H-bonds generated for 'chain 'F' and resid 346 through 348' 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 455 removed outlier: 3.527A pdb=" N LEU F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 472 through 476 removed outlier: 3.523A pdb=" N GLU F 476 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.157A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 509 through 517 removed outlier: 4.106A 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 563 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 640 through 645 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: 3.525A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.573A pdb=" N ALA G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 Processing helix chain 'G' and resid 242 through 256 removed outlier: 3.651A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.818A 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 409 Processing helix chain 'G' and resid 460 through 463 removed outlier: 3.981A pdb=" N LEU G 463 " --> pdb=" O ASP G 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 460 through 463' Processing helix chain 'G' and resid 500 through 509 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.570A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 523 Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.631A pdb=" N GLN G 537 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 552 Processing helix chain 'G' and resid 556 through 566 Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.677A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 253 Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.637A pdb=" N VAL J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 160 removed outlier: 4.401A pdb=" N TYR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.941A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 7.999A pdb=" N CYS A 92 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 37 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156 removed outlier: 4.734A pdb=" N ALA A 187 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG A 123 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N ASP A 189 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N SER A 125 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N ILE A 191 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LEU A 127 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N HIS A 193 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 279 removed outlier: 3.542A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 3.730A pdb=" N GLU A 480 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.411A pdb=" N GLY B 250 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL B 377 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 276 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.635A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR B 633 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 526 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.639A pdb=" N PHE C 162 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL C 175 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 127 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 124 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.801A pdb=" N ARG C 154 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.387A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 548 through 552 removed outlier: 6.945A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.907A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 548 through 552 removed outlier: 6.867A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 312 through 314 removed outlier: 7.485A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY E 250 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.621A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.751A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 548 through 552 removed outlier: 6.927A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.233A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 451 " --> pdb=" O TYR G 439 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE G 447 " --> pdb=" O ASN G 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 382 through 386 removed outlier: 6.806A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 295 through 297 Processing sheet with id=AC3, first strand: chain 'G' and resid 399 through 400 Processing sheet with id=AC4, first strand: chain 'G' and resid 422 through 424 removed outlier: 3.720A pdb=" N PHE G 457 " --> pdb=" O ALA G 423 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 112 through 116 removed outlier: 3.893A pdb=" N SER J 165 " --> pdb=" O GLN J 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 216 removed outlier: 4.026A pdb=" N SER K 265 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU K 243 " --> pdb=" O LEU K 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE K 245 " --> pdb=" O LYS K 248 " (cutoff:3.500A) 1586 hydrogen bonds defined for protein. 4503 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: 5.96 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11534 1.34 - 1.46: 6574 1.46 - 1.58: 16196 1.58 - 1.69: 46 1.69 - 1.81: 288 Bond restraints: 34638 Sorted by residual: bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+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 3.03e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 34633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 46370 2.14 - 4.29: 395 4.29 - 6.43: 74 6.43 - 8.57: 17 8.57 - 10.72: 14 Bond angle restraints: 46870 Sorted by residual: angle pdb=" N GLY G 323 " pdb=" CA GLY G 323 " pdb=" C GLY G 323 " ideal model delta sigma weight residual 110.96 115.83 -4.87 1.19e+00 7.06e-01 1.68e+01 angle pdb=" C1' ADP E 902 " pdb=" C2' ADP E 902 " pdb=" C3' ADP E 902 " ideal model delta sigma weight residual 111.00 100.28 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ALA B 23 " pdb=" CA ALA B 23 " pdb=" C ALA B 23 " ideal model delta sigma weight residual 111.28 107.58 3.70 1.09e+00 8.42e-01 1.15e+01 angle pdb=" N ILE B 26 " pdb=" CA ILE B 26 " pdb=" C ILE B 26 " ideal model delta sigma weight residual 112.12 109.27 2.85 8.40e-01 1.42e+00 1.15e+01 angle pdb=" PA ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sigma weight residual 120.50 130.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 46865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 20925 28.56 - 57.11: 315 57.11 - 85.67: 16 85.67 - 114.22: 5 114.22 - 142.78: 9 Dihedral angle restraints: 21270 sinusoidal: 8799 harmonic: 12471 Sorted by residual: dihedral pdb=" C2' ADP C 901 " pdb=" C1' ADP C 901 " pdb=" N9 ADP C 901 " pdb=" C4 ADP C 901 " ideal model delta sinusoidal sigma weight residual 91.55 -125.68 -142.78 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -136.31 -132.15 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C4' ADP E 902 " pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " ideal model delta sinusoidal sigma weight residual 180.00 49.18 130.82 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 21267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4718 0.068 - 0.135: 522 0.135 - 0.203: 13 0.203 - 0.270: 5 0.270 - 0.338: 11 Chirality restraints: 5269 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 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+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 2.06e+00 ... (remaining 5266 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 554 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 555 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 234 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C LEU C 234 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU C 234 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG C 235 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 298 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS F 298 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS F 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA F 299 " -0.008 2.00e-02 2.50e+03 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 352 2.53 - 3.13: 28705 3.13 - 3.72: 52282 3.72 - 4.31: 69432 4.31 - 4.90: 119396 Nonbonded interactions: 270167 Sorted by model distance: nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.942 3.040 nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.953 3.040 nonbonded pdb=" O GLN K 262 " pdb=" OG SER K 265 " model vdw 1.953 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 1.988 3.040 nonbonded pdb=" OG1 THR B 262 " pdb=" O3G ATP B 901 " model vdw 1.997 3.040 ... (remaining 270162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 786 or resid 902)) selection = (chain 'C' and (resid 33 through 786 or resid 902)) } ncs_group { reference = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and resid 208 through 902) selection = (chain 'E' and resid 208 through 902) selection = (chain 'F' and (resid 208 through 787 or resid 901 through 902)) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 201 through 273) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.600 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.887 34648 Z= 0.504 Angle : 0.548 10.715 46876 Z= 0.262 Chirality : 0.043 0.338 5269 Planarity : 0.003 0.038 6107 Dihedral : 10.488 142.777 13196 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.89 % Allowed : 5.33 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.14), residues: 4259 helix: 2.23 (0.12), residues: 2036 sheet: -0.64 (0.21), residues: 615 loop : 0.30 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 131 TYR 0.011 0.001 TYR B 254 PHE 0.010 0.001 PHE D 275 TRP 0.007 0.001 TRP E 486 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (34638) covalent geometry : angle 0.54734 / 0.26 (46870) hydrogen bonds : bond 0.14818 / 9.78 ( 1586) hydrogen bonds : angle 5.47046 / 3.93 ( 4503) metal coordination : bond 0.08341 / 4.13 ( 8) metal coordination : angle 2.62217 / 1.42 ( 6) Misc. bond : bond 0.62969 / 33.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 564 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6856 (mmtt) REVERT: A 92 CYS cc_start: 0.6666 (p) cc_final: 0.6357 (p) REVERT: A 168 MET cc_start: 0.6996 (ppp) cc_final: 0.6732 (ppp) REVERT: A 305 LYS cc_start: 0.8289 (pptt) cc_final: 0.7930 (mmtt) REVERT: A 314 ASP cc_start: 0.8813 (t0) cc_final: 0.8605 (t0) REVERT: A 359 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8039 (mtp-110) REVERT: B 774 LEU cc_start: 0.8717 (tp) cc_final: 0.8452 (tp) REVERT: B 778 GLU cc_start: 0.8688 (tp30) cc_final: 0.8459 (pt0) REVERT: C 253 MET cc_start: 0.8341 (mtp) cc_final: 0.8023 (mtp) REVERT: C 430 MET cc_start: 0.8746 (tpt) cc_final: 0.8487 (tpp) REVERT: C 474 LEU cc_start: 0.8716 (mm) cc_final: 0.8416 (pt) REVERT: D 514 THR cc_start: 0.8738 (m) cc_final: 0.8501 (p) REVERT: D 556 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8081 (mp0) REVERT: E 314 ASP cc_start: 0.8893 (t0) cc_final: 0.8622 (t0) REVERT: E 359 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7163 (mtp85) REVERT: E 430 MET cc_start: 0.9198 (tpp) cc_final: 0.8985 (tpp) REVERT: E 556 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8410 (mt-10) REVERT: E 618 MET cc_start: 0.8977 (ttp) cc_final: 0.8665 (ttm) REVERT: F 246 LYS cc_start: 0.8017 (tptp) cc_final: 0.7742 (tmtt) REVERT: F 314 ASP cc_start: 0.8865 (t0) cc_final: 0.8520 (t0) REVERT: F 324 ASP cc_start: 0.6719 (t0) cc_final: 0.6518 (t0) REVERT: F 348 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7607 (mtm-85) REVERT: F 556 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8527 (mm-30) REVERT: G 254 TYR cc_start: 0.7742 (t80) cc_final: 0.7376 (t80) REVERT: G 293 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8026 (tp-100) REVERT: G 316 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5654 (mm-30) REVERT: G 344 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7122 (p-80) REVERT: G 378 SER cc_start: 0.6989 (m) cc_final: 0.6763 (m) REVERT: G 445 TYR cc_start: 0.7802 (m-80) cc_final: 0.7159 (m-80) REVERT: G 553 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7527 (tttm) outliers start: 69 outliers final: 22 residues processed: 611 average time/residue: 0.2630 time to fit residues: 247.0173 Evaluate side-chains 325 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.9990 chunk 155 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 206 ASN C 394 HIS D 225 GLN D 670 GLN E 337 GLN F 548 ASN G 344 HIS G 361 HIS G 491 ASN G 528 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090554 restraints weight = 87469.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092341 restraints weight = 44788.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093551 restraints weight = 29005.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093853 restraints weight = 23418.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094000 restraints weight = 22014.757| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34648 Z= 0.138 Angle : 0.636 10.937 46876 Z= 0.310 Chirality : 0.044 0.180 5269 Planarity : 0.004 0.052 6107 Dihedral : 8.057 135.917 4814 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.97 % Allowed : 8.94 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 4259 helix: 1.99 (0.12), residues: 2068 sheet: -0.25 (0.21), residues: 598 loop : 0.30 (0.17), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 672 TYR 0.014 0.001 TYR A 416 PHE 0.024 0.002 PHE A 141 TRP 0.011 0.001 TRP E 486 HIS 0.008 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (34638) covalent geometry : angle 0.63505 / 0.31 (46870) hydrogen bonds : bond 0.03890 / 2.55 ( 1586) hydrogen bonds : angle 4.50540 / 3.20 ( 4503) metal coordination : bond 0.01472 / 0.64 ( 8) metal coordination : angle 2.83372 / 1.91 ( 6) Misc. bond : bond 0.00755 / 0.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 336 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6941 (ppp) cc_final: 0.5241 (mmt) REVERT: A 314 ASP cc_start: 0.8669 (t0) cc_final: 0.8411 (t0) REVERT: A 359 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8005 (mtp-110) REVERT: A 476 GLU cc_start: 0.7366 (pm20) cc_final: 0.7153 (pm20) REVERT: B 208 MET cc_start: 0.5579 (mmp) cc_final: 0.4818 (tpt) REVERT: B 342 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: B 348 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7972 (ptp90) REVERT: B 574 ASP cc_start: 0.8646 (m-30) cc_final: 0.8395 (t0) REVERT: B 773 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7299 (mm-30) REVERT: B 774 LEU cc_start: 0.8712 (tp) cc_final: 0.8448 (tp) REVERT: C 96 ARG cc_start: 0.6951 (tpm170) cc_final: 0.6649 (mtp-110) REVERT: C 202 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: C 253 MET cc_start: 0.8220 (mtp) cc_final: 0.7874 (mtp) REVERT: C 348 ARG cc_start: 0.6916 (tpp-160) cc_final: 0.6397 (ptp-170) REVERT: C 474 LEU cc_start: 0.8782 (mm) cc_final: 0.8462 (pt) REVERT: D 208 MET cc_start: 0.6396 (ppp) cc_final: 0.5502 (tpt) REVERT: D 304 GLU cc_start: 0.8433 (tp30) cc_final: 0.8019 (mm-30) REVERT: D 348 ARG cc_start: 0.6961 (ptt-90) cc_final: 0.6690 (ptp90) REVERT: D 359 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: D 514 THR cc_start: 0.8563 (m) cc_final: 0.8320 (p) REVERT: D 556 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8093 (mp0) REVERT: E 364 ASP cc_start: 0.8932 (t0) cc_final: 0.8731 (t0) REVERT: E 378 ASP cc_start: 0.8167 (t0) cc_final: 0.7903 (t0) REVERT: E 556 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8225 (mt-10) REVERT: E 635 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7572 (mmm160) REVERT: E 689 THR cc_start: 0.8649 (p) cc_final: 0.8410 (p) REVERT: F 246 LYS cc_start: 0.8153 (tptp) cc_final: 0.7787 (tmtt) REVERT: F 315 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7673 (tp30) REVERT: F 556 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8053 (tp30) REVERT: F 762 MET cc_start: 0.8111 (ptm) cc_final: 0.7643 (ptm) REVERT: G 187 SER cc_start: 0.6979 (t) cc_final: 0.6726 (m) REVERT: G 242 SER cc_start: 0.8523 (m) cc_final: 0.8119 (p) REVERT: G 254 TYR cc_start: 0.7791 (t80) cc_final: 0.7334 (t80) REVERT: J 158 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6960 (p0) outliers start: 72 outliers final: 32 residues processed: 388 average time/residue: 0.2285 time to fit residues: 142.9395 Evaluate side-chains 323 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 362 optimal weight: 0.6980 chunk 423 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 283 optimal weight: 0.0980 chunk 229 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 651 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.120789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090649 restraints weight = 87063.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093406 restraints weight = 43747.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095044 restraints weight = 26351.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094927 restraints weight = 22320.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094788 restraints weight = 19904.329| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34648 Z= 0.134 Angle : 0.596 11.686 46876 Z= 0.289 Chirality : 0.043 0.190 5269 Planarity : 0.004 0.054 6107 Dihedral : 7.504 135.576 4784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.75 % Allowed : 10.23 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 4259 helix: 1.87 (0.12), residues: 2068 sheet: -0.13 (0.21), residues: 596 loop : 0.26 (0.17), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG C 99 TYR 0.016 0.001 TYR G 439 PHE 0.013 0.001 PHE E 549 TRP 0.012 0.001 TRP E 486 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (34638) covalent geometry : angle 0.59472 / 0.29 (46870) hydrogen bonds : bond 0.03517 / 2.32 ( 1586) hydrogen bonds : angle 4.30932 / 3.08 ( 4503) metal coordination : bond 0.02430 / 1.03 ( 8) metal coordination : angle 3.62725 / 2.91 ( 6) Misc. bond : bond 0.00151 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6860 (ppp) cc_final: 0.5246 (mmt) REVERT: A 359 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7984 (mtp-110) REVERT: A 476 GLU cc_start: 0.7266 (pm20) cc_final: 0.7016 (pm20) REVERT: B 208 MET cc_start: 0.5656 (mmp) cc_final: 0.5041 (tpt) REVERT: B 215 ASP cc_start: 0.9097 (t0) cc_final: 0.8830 (t0) REVERT: B 285 MET cc_start: 0.8880 (mmm) cc_final: 0.8663 (mmt) REVERT: B 574 ASP cc_start: 0.8598 (m-30) cc_final: 0.8344 (t0) REVERT: C 253 MET cc_start: 0.8228 (mtp) cc_final: 0.7893 (mtp) REVERT: C 474 LEU cc_start: 0.8721 (mm) cc_final: 0.8448 (pt) REVERT: C 651 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: D 304 GLU cc_start: 0.8418 (tp30) cc_final: 0.8035 (mm-30) REVERT: D 514 THR cc_start: 0.8567 (m) cc_final: 0.8328 (p) REVERT: D 556 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8055 (mp0) REVERT: E 285 MET cc_start: 0.8584 (mmm) cc_final: 0.8312 (mmm) REVERT: E 314 ASP cc_start: 0.8835 (t0) cc_final: 0.8342 (m-30) REVERT: E 342 MET cc_start: 0.8703 (mtp) cc_final: 0.8446 (mtp) REVERT: E 556 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8292 (mt-10) REVERT: E 635 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7746 (mmm160) REVERT: F 223 MET cc_start: 0.8910 (tpp) cc_final: 0.8441 (tpp) REVERT: F 246 LYS cc_start: 0.8172 (tptp) cc_final: 0.7904 (tmtt) REVERT: F 315 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7695 (tp30) REVERT: F 762 MET cc_start: 0.8013 (ptm) cc_final: 0.7533 (ptm) REVERT: F 782 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8785 (tm-30) REVERT: G 187 SER cc_start: 0.7074 (t) cc_final: 0.6853 (m) REVERT: G 242 SER cc_start: 0.8503 (m) cc_final: 0.8132 (p) REVERT: G 254 TYR cc_start: 0.7769 (t80) cc_final: 0.7326 (t80) REVERT: H 238 MET cc_start: 0.8080 (ttm) cc_final: 0.7665 (tpp) REVERT: J 158 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6883 (p0) outliers start: 64 outliers final: 37 residues processed: 351 average time/residue: 0.2181 time to fit residues: 125.2064 Evaluate side-chains 307 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 126 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 210 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN G 362 GLN H 298 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.119966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089824 restraints weight = 86950.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091838 restraints weight = 45435.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092929 restraints weight = 30455.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093003 restraints weight = 24442.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093311 restraints weight = 22968.787| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34648 Z= 0.151 Angle : 0.590 11.948 46876 Z= 0.284 Chirality : 0.043 0.172 5269 Planarity : 0.004 0.053 6107 Dihedral : 7.362 137.099 4781 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.16 % Allowed : 10.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4259 helix: 1.79 (0.12), residues: 2072 sheet: -0.17 (0.21), residues: 590 loop : 0.22 (0.17), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 359 TYR 0.017 0.001 TYR G 439 PHE 0.025 0.001 PHE E 585 TRP 0.013 0.001 TRP E 486 HIS 0.009 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (34638) covalent geometry : angle 0.58801 / 0.28 (46870) hydrogen bonds : bond 0.03439 / 2.27 ( 1586) hydrogen bonds : angle 4.20801 / 3.01 ( 4503) metal coordination : bond 0.02820 / 1.16 ( 8) metal coordination : angle 4.23366 / 3.48 ( 6) Misc. bond : bond 0.00020 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7026 (ppp) cc_final: 0.5301 (mmt) REVERT: A 359 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8040 (mtp-110) REVERT: A 476 GLU cc_start: 0.7325 (pm20) cc_final: 0.7075 (pm20) REVERT: B 215 ASP cc_start: 0.9134 (t0) cc_final: 0.8896 (t0) REVERT: B 285 MET cc_start: 0.8912 (mmm) cc_final: 0.8701 (mmt) REVERT: B 342 MET cc_start: 0.9099 (mtp) cc_final: 0.8373 (mtp) REVERT: B 556 GLU cc_start: 0.8647 (tp30) cc_final: 0.8354 (tp30) REVERT: B 574 ASP cc_start: 0.8661 (m-30) cc_final: 0.8446 (t0) REVERT: C 253 MET cc_start: 0.8277 (mtp) cc_final: 0.7946 (mtp) REVERT: C 474 LEU cc_start: 0.8726 (mm) cc_final: 0.8396 (pp) REVERT: C 651 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: D 208 MET cc_start: 0.6199 (ppp) cc_final: 0.5227 (tpt) REVERT: D 223 MET cc_start: 0.8625 (mmm) cc_final: 0.8396 (tpp) REVERT: D 304 GLU cc_start: 0.8516 (tp30) cc_final: 0.8088 (mm-30) REVERT: D 359 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7765 (mtm-85) REVERT: D 514 THR cc_start: 0.8585 (m) cc_final: 0.8348 (p) REVERT: D 556 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8051 (mp0) REVERT: E 314 ASP cc_start: 0.8914 (t0) cc_final: 0.8405 (m-30) REVERT: E 342 MET cc_start: 0.8776 (mtp) cc_final: 0.8440 (mtp) REVERT: E 556 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8254 (mt-10) REVERT: E 635 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7733 (mmm160) REVERT: F 223 MET cc_start: 0.8890 (tpp) cc_final: 0.8402 (tpp) REVERT: F 246 LYS cc_start: 0.8191 (tptp) cc_final: 0.7957 (tmtt) REVERT: F 315 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7724 (tp30) REVERT: F 762 MET cc_start: 0.8025 (ptm) cc_final: 0.7481 (ptm) REVERT: G 187 SER cc_start: 0.7164 (t) cc_final: 0.6942 (m) REVERT: G 242 SER cc_start: 0.8518 (m) cc_final: 0.8022 (t) REVERT: G 553 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7185 (tttt) REVERT: H 238 MET cc_start: 0.8260 (ttm) cc_final: 0.7794 (tpp) REVERT: J 158 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6960 (p0) outliers start: 79 outliers final: 42 residues processed: 345 average time/residue: 0.2146 time to fit residues: 122.4080 Evaluate side-chains 307 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 492 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 635 ARG Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 553 LYS Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 296 optimal weight: 0.2980 chunk 363 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 390 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 412 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 206 ASN C 193 HIS D 548 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.120695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090635 restraints weight = 86601.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093455 restraints weight = 43138.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094092 restraints weight = 26253.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094316 restraints weight = 23966.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094331 restraints weight = 21725.462| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34648 Z= 0.116 Angle : 0.574 13.264 46876 Z= 0.274 Chirality : 0.042 0.219 5269 Planarity : 0.004 0.051 6107 Dihedral : 7.208 137.406 4778 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.11 % Allowed : 11.46 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4259 helix: 1.81 (0.12), residues: 2069 sheet: -0.05 (0.21), residues: 587 loop : 0.23 (0.17), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 767 TYR 0.017 0.001 TYR G 439 PHE 0.019 0.001 PHE E 585 TRP 0.011 0.001 TRP E 486 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (34638) covalent geometry : angle 0.57262 / 0.27 (46870) hydrogen bonds : bond 0.03155 / 2.08 ( 1586) hydrogen bonds : angle 4.10706 / 2.94 ( 4503) metal coordination : bond 0.02027 / 0.82 ( 8) metal coordination : angle 3.75571 / 3.06 ( 6) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6983 (ppp) cc_final: 0.5220 (mmt) REVERT: A 202 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6142 (mt-10) REVERT: A 359 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.8025 (mtp-110) REVERT: A 618 MET cc_start: 0.8946 (ttp) cc_final: 0.8733 (ttp) REVERT: B 206 ASN cc_start: 0.3149 (OUTLIER) cc_final: 0.2914 (p0) REVERT: B 215 ASP cc_start: 0.9079 (t0) cc_final: 0.8843 (t0) REVERT: B 342 MET cc_start: 0.9062 (mtp) cc_final: 0.8306 (mtp) REVERT: B 348 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7540 (ptp-170) REVERT: B 574 ASP cc_start: 0.8613 (m-30) cc_final: 0.8371 (t0) REVERT: C 474 LEU cc_start: 0.8684 (mm) cc_final: 0.8320 (pp) REVERT: D 208 MET cc_start: 0.6270 (ppp) cc_final: 0.5262 (tpt) REVERT: D 223 MET cc_start: 0.8605 (mmm) cc_final: 0.8379 (tpp) REVERT: D 304 GLU cc_start: 0.8427 (tp30) cc_final: 0.8013 (mm-30) REVERT: D 514 THR cc_start: 0.8581 (m) cc_final: 0.8348 (p) REVERT: D 556 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8018 (mp0) REVERT: E 223 MET cc_start: 0.8459 (tpp) cc_final: 0.8194 (mmm) REVERT: E 285 MET cc_start: 0.8539 (tpp) cc_final: 0.7949 (tpp) REVERT: E 314 ASP cc_start: 0.8888 (t0) cc_final: 0.8345 (m-30) REVERT: E 317 ASP cc_start: 0.8284 (t0) cc_final: 0.7921 (p0) REVERT: E 332 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: E 342 MET cc_start: 0.8759 (mtp) cc_final: 0.8402 (mtp) REVERT: E 556 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8192 (mt-10) REVERT: E 617 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: F 223 MET cc_start: 0.8747 (tpp) cc_final: 0.8460 (tpp) REVERT: F 246 LYS cc_start: 0.8115 (tptp) cc_final: 0.7867 (tmtt) REVERT: F 315 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7696 (tp30) REVERT: F 343 ASP cc_start: 0.8362 (m-30) cc_final: 0.8115 (m-30) REVERT: F 762 MET cc_start: 0.7952 (ptm) cc_final: 0.7485 (ptm) REVERT: G 242 SER cc_start: 0.8488 (m) cc_final: 0.7914 (t) REVERT: G 254 TYR cc_start: 0.7919 (t80) cc_final: 0.7483 (t80) REVERT: G 344 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7157 (p90) REVERT: H 238 MET cc_start: 0.8245 (ttm) cc_final: 0.7757 (tpp) outliers start: 77 outliers final: 47 residues processed: 342 average time/residue: 0.2151 time to fit residues: 121.5397 Evaluate side-chains 311 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 31 optimal weight: 0.2980 chunk 335 optimal weight: 2.9990 chunk 381 optimal weight: 0.9980 chunk 59 optimal weight: 0.0670 chunk 101 optimal weight: 0.1980 chunk 173 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 403 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 716 HIS B 206 ASN C 790 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091538 restraints weight = 86048.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094500 restraints weight = 42733.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095156 restraints weight = 25843.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095343 restraints weight = 23342.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095483 restraints weight = 21203.116| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34648 Z= 0.100 Angle : 0.564 13.866 46876 Z= 0.266 Chirality : 0.042 0.184 5269 Planarity : 0.003 0.050 6107 Dihedral : 7.015 137.094 4776 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.94 % Allowed : 11.73 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 4259 helix: 1.83 (0.12), residues: 2070 sheet: 0.06 (0.21), residues: 587 loop : 0.24 (0.17), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 359 TYR 0.017 0.001 TYR G 439 PHE 0.017 0.001 PHE G 340 TRP 0.009 0.001 TRP B 561 HIS 0.012 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (34638) covalent geometry : angle 0.56233 / 0.27 (46870) hydrogen bonds : bond 0.02893 / 1.91 ( 1586) hydrogen bonds : angle 3.98327 / 2.85 ( 4503) metal coordination : bond 0.01697 / 0.69 ( 8) metal coordination : angle 3.34143 / 2.70 ( 6) Misc. bond : bond 0.00080 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 293 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6930 (ppp) cc_final: 0.5168 (mmt) REVERT: A 202 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6045 (mt-10) REVERT: A 331 GLU cc_start: 0.6913 (pt0) cc_final: 0.6527 (pt0) REVERT: A 359 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7969 (mtp-110) REVERT: A 566 GLU cc_start: 0.7513 (mp0) cc_final: 0.7151 (mp0) REVERT: B 206 ASN cc_start: 0.2364 (OUTLIER) cc_final: 0.1844 (p0) REVERT: B 208 MET cc_start: 0.4447 (tpt) cc_final: 0.4213 (mmp) REVERT: B 342 MET cc_start: 0.9046 (mtp) cc_final: 0.8224 (mtp) REVERT: B 348 ARG cc_start: 0.8248 (ptp90) cc_final: 0.7570 (ptp-170) REVERT: B 574 ASP cc_start: 0.8595 (m-30) cc_final: 0.8375 (t0) REVERT: C 474 LEU cc_start: 0.8698 (mm) cc_final: 0.8304 (pp) REVERT: C 651 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: D 208 MET cc_start: 0.6060 (ppp) cc_final: 0.5134 (tpt) REVERT: D 223 MET cc_start: 0.8584 (mmm) cc_final: 0.8343 (tpp) REVERT: D 304 GLU cc_start: 0.8339 (tp30) cc_final: 0.7931 (mm-30) REVERT: D 342 MET cc_start: 0.9257 (tpp) cc_final: 0.8990 (tpp) REVERT: D 359 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7648 (mtm-85) REVERT: D 514 THR cc_start: 0.8566 (m) cc_final: 0.8332 (p) REVERT: D 556 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8026 (mp0) REVERT: E 223 MET cc_start: 0.8384 (tpp) cc_final: 0.8171 (mmm) REVERT: E 331 GLU cc_start: 0.8234 (mp0) cc_final: 0.7883 (pm20) REVERT: E 342 MET cc_start: 0.8766 (mtp) cc_final: 0.8391 (mtp) REVERT: E 430 MET cc_start: 0.9287 (tpp) cc_final: 0.9011 (tpp) REVERT: E 556 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8198 (mt-10) REVERT: F 223 MET cc_start: 0.8659 (tpp) cc_final: 0.8451 (tpp) REVERT: F 315 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7707 (tp30) REVERT: F 343 ASP cc_start: 0.8330 (m-30) cc_final: 0.8076 (m-30) REVERT: F 762 MET cc_start: 0.7924 (ptm) cc_final: 0.7448 (ptm) REVERT: G 242 SER cc_start: 0.8386 (m) cc_final: 0.7879 (t) REVERT: G 254 TYR cc_start: 0.7888 (t80) cc_final: 0.7462 (t80) REVERT: G 344 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.6762 (p90) REVERT: G 549 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6973 (mm-30) outliers start: 71 outliers final: 50 residues processed: 351 average time/residue: 0.2004 time to fit residues: 116.1541 Evaluate side-chains 328 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 231 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 300 optimal weight: 9.9990 chunk 324 optimal weight: 0.0670 chunk 97 optimal weight: 0.3980 chunk 142 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091176 restraints weight = 87026.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094223 restraints weight = 43221.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094955 restraints weight = 25968.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095077 restraints weight = 23225.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095025 restraints weight = 21052.979| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34648 Z= 0.109 Angle : 0.572 15.748 46876 Z= 0.271 Chirality : 0.042 0.200 5269 Planarity : 0.003 0.049 6107 Dihedral : 6.934 136.894 4776 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.94 % Allowed : 12.20 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.13), residues: 4259 helix: 1.83 (0.12), residues: 2072 sheet: 0.11 (0.21), residues: 587 loop : 0.25 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 359 TYR 0.016 0.001 TYR G 439 PHE 0.018 0.001 PHE G 340 TRP 0.010 0.001 TRP E 486 HIS 0.007 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (34638) covalent geometry : angle 0.57044 / 0.27 (46870) hydrogen bonds : bond 0.02892 / 1.91 ( 1586) hydrogen bonds : angle 3.95903 / 2.84 ( 4503) metal coordination : bond 0.01953 / 0.79 ( 8) metal coordination : angle 3.33609 / 2.71 ( 6) Misc. bond : bond 0.00082 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6950 (ppp) cc_final: 0.5219 (mmt) REVERT: A 202 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6062 (mt-10) REVERT: A 331 GLU cc_start: 0.7050 (pt0) cc_final: 0.6681 (pt0) REVERT: A 359 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7972 (mtp-110) REVERT: A 566 GLU cc_start: 0.7615 (mp0) cc_final: 0.7247 (mp0) REVERT: B 208 MET cc_start: 0.4659 (tpt) cc_final: 0.4324 (mmp) REVERT: B 246 LYS cc_start: 0.8901 (mmpt) cc_final: 0.8650 (mmmt) REVERT: B 293 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: B 342 MET cc_start: 0.9029 (mtp) cc_final: 0.8222 (mtp) REVERT: B 348 ARG cc_start: 0.8254 (ptp90) cc_final: 0.7570 (ptp-170) REVERT: B 574 ASP cc_start: 0.8599 (m-30) cc_final: 0.8375 (t0) REVERT: C 474 LEU cc_start: 0.8703 (mm) cc_final: 0.8286 (pp) REVERT: C 651 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: D 208 MET cc_start: 0.6231 (ppp) cc_final: 0.5311 (tpt) REVERT: D 223 MET cc_start: 0.8610 (mmm) cc_final: 0.8384 (tpp) REVERT: D 304 GLU cc_start: 0.8353 (tp30) cc_final: 0.7948 (mm-30) REVERT: D 359 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7580 (mtm-85) REVERT: D 514 THR cc_start: 0.8570 (m) cc_final: 0.8347 (p) REVERT: D 556 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7992 (mp0) REVERT: E 223 MET cc_start: 0.8390 (tpp) cc_final: 0.8185 (mmm) REVERT: E 314 ASP cc_start: 0.8801 (t0) cc_final: 0.8356 (m-30) REVERT: E 331 GLU cc_start: 0.8234 (mp0) cc_final: 0.7873 (pm20) REVERT: E 332 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7436 (ttm-80) REVERT: E 342 MET cc_start: 0.8761 (mtp) cc_final: 0.8373 (mtp) REVERT: F 315 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7713 (tp30) REVERT: F 493 ASP cc_start: 0.8714 (m-30) cc_final: 0.8378 (t70) REVERT: F 762 MET cc_start: 0.7920 (ptm) cc_final: 0.7441 (ptm) REVERT: G 242 SER cc_start: 0.8394 (m) cc_final: 0.7896 (t) REVERT: G 549 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7031 (mm-30) outliers start: 71 outliers final: 53 residues processed: 338 average time/residue: 0.1997 time to fit residues: 111.8610 Evaluate side-chains 327 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 93 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 22 optimal weight: 0.0040 chunk 191 optimal weight: 7.9990 chunk 424 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 169 optimal weight: 0.0570 chunk 188 optimal weight: 0.0030 chunk 420 optimal weight: 6.9990 chunk 411 optimal weight: 3.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 432 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.120171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090302 restraints weight = 86853.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091995 restraints weight = 45190.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093787 restraints weight = 29585.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093709 restraints weight = 23119.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093650 restraints weight = 21452.599| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34648 Z= 0.142 Angle : 0.591 15.952 46876 Z= 0.282 Chirality : 0.042 0.193 5269 Planarity : 0.004 0.050 6107 Dihedral : 6.931 137.547 4774 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.00 % Allowed : 12.41 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4259 helix: 1.78 (0.12), residues: 2074 sheet: 0.07 (0.21), residues: 587 loop : 0.22 (0.17), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 359 TYR 0.015 0.001 TYR G 439 PHE 0.016 0.001 PHE G 340 TRP 0.013 0.001 TRP E 486 HIS 0.014 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (34638) covalent geometry : angle 0.58888 / 0.28 (46870) hydrogen bonds : bond 0.03140 / 2.07 ( 1586) hydrogen bonds : angle 4.03177 / 2.89 ( 4503) metal coordination : bond 0.02668 / 1.09 ( 8) metal coordination : angle 4.10962 / 3.32 ( 6) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7059 (ppp) cc_final: 0.5215 (mmt) REVERT: A 314 ASP cc_start: 0.8798 (t0) cc_final: 0.8539 (t0) REVERT: A 331 GLU cc_start: 0.7264 (pt0) cc_final: 0.6943 (pt0) REVERT: A 359 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.8034 (mtp-110) REVERT: A 566 GLU cc_start: 0.7640 (mp0) cc_final: 0.7266 (mp0) REVERT: A 618 MET cc_start: 0.8818 (ttp) cc_final: 0.8528 (ttp) REVERT: B 246 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8662 (mmmt) REVERT: B 293 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: B 342 MET cc_start: 0.9044 (mtp) cc_final: 0.8307 (mtp) REVERT: B 574 ASP cc_start: 0.8640 (m-30) cc_final: 0.8394 (t0) REVERT: C 474 LEU cc_start: 0.8699 (mm) cc_final: 0.8268 (pp) REVERT: C 651 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: D 208 MET cc_start: 0.6280 (ppp) cc_final: 0.6020 (ppp) REVERT: D 223 MET cc_start: 0.8605 (mmm) cc_final: 0.8375 (tpp) REVERT: D 304 GLU cc_start: 0.8444 (tp30) cc_final: 0.8107 (mm-30) REVERT: D 514 THR cc_start: 0.8617 (m) cc_final: 0.8357 (p) REVERT: D 556 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8062 (mp0) REVERT: E 223 MET cc_start: 0.8413 (tpp) cc_final: 0.8197 (mmm) REVERT: E 254 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7890 (p90) REVERT: E 314 ASP cc_start: 0.8834 (t0) cc_final: 0.8376 (m-30) REVERT: E 331 GLU cc_start: 0.8243 (mp0) cc_final: 0.7850 (pm20) REVERT: E 332 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7428 (ttm-80) REVERT: E 342 MET cc_start: 0.8760 (mtp) cc_final: 0.8280 (mtp) REVERT: F 315 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7724 (tp30) REVERT: F 430 MET cc_start: 0.8149 (tmm) cc_final: 0.7912 (tmm) REVERT: F 493 ASP cc_start: 0.8717 (m-30) cc_final: 0.8374 (t70) REVERT: G 242 SER cc_start: 0.8458 (m) cc_final: 0.7977 (t) REVERT: G 344 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6718 (p90) REVERT: G 422 MET cc_start: 0.8500 (tpp) cc_final: 0.8254 (tpp) REVERT: H 281 MET cc_start: 0.2138 (mmp) cc_final: 0.1795 (mmp) outliers start: 73 outliers final: 50 residues processed: 330 average time/residue: 0.2004 time to fit residues: 109.0201 Evaluate side-chains 318 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 301 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 127 optimal weight: 20.0000 chunk 336 optimal weight: 0.5980 chunk 205 optimal weight: 0.0010 chunk 123 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 331 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090910 restraints weight = 86515.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093779 restraints weight = 43498.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094691 restraints weight = 26065.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094806 restraints weight = 23321.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094747 restraints weight = 21050.887| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 34648 Z= 0.106 Angle : 0.585 17.427 46876 Z= 0.276 Chirality : 0.042 0.214 5269 Planarity : 0.003 0.049 6107 Dihedral : 6.862 139.254 4774 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.67 % Allowed : 12.88 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.13), residues: 4259 helix: 1.79 (0.12), residues: 2068 sheet: 0.16 (0.21), residues: 587 loop : 0.23 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 359 TYR 0.016 0.001 TYR G 439 PHE 0.014 0.001 PHE G 340 TRP 0.009 0.001 TRP E 486 HIS 0.017 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (34638) covalent geometry : angle 0.58328 / 0.28 (46870) hydrogen bonds : bond 0.02910 / 1.92 ( 1586) hydrogen bonds : angle 3.94917 / 2.83 ( 4503) metal coordination : bond 0.01847 / 0.75 ( 8) metal coordination : angle 3.62581 / 2.95 ( 6) Misc. bond : bond 0.00077 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6902 (ppp) cc_final: 0.5127 (mmt) REVERT: A 331 GLU cc_start: 0.7209 (pt0) cc_final: 0.6885 (pt0) REVERT: A 359 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.8034 (mtp-110) REVERT: A 618 MET cc_start: 0.8851 (ttp) cc_final: 0.8545 (ttp) REVERT: B 208 MET cc_start: 0.4449 (tpt) cc_final: 0.4173 (mmp) REVERT: B 246 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8640 (mmmt) REVERT: B 293 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: B 342 MET cc_start: 0.9005 (mtp) cc_final: 0.8277 (mtp) REVERT: B 348 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7689 (ptt180) REVERT: B 574 ASP cc_start: 0.8585 (m-30) cc_final: 0.8362 (t0) REVERT: C 474 LEU cc_start: 0.8689 (mm) cc_final: 0.8270 (pp) REVERT: C 651 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: D 208 MET cc_start: 0.6224 (ppp) cc_final: 0.6005 (ppp) REVERT: D 223 MET cc_start: 0.8605 (mmm) cc_final: 0.8353 (tpp) REVERT: D 304 GLU cc_start: 0.8297 (tp30) cc_final: 0.7949 (mm-30) REVERT: D 323 ARG cc_start: 0.7600 (tmt170) cc_final: 0.7204 (tmt170) REVERT: D 359 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: D 514 THR cc_start: 0.8568 (m) cc_final: 0.8333 (p) REVERT: D 556 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8040 (mp0) REVERT: E 314 ASP cc_start: 0.8746 (t0) cc_final: 0.8288 (m-30) REVERT: E 331 GLU cc_start: 0.8208 (mp0) cc_final: 0.7850 (pm20) REVERT: E 332 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: E 342 MET cc_start: 0.8715 (mtp) cc_final: 0.8247 (mtp) REVERT: F 253 MET cc_start: 0.8454 (mtm) cc_final: 0.8238 (mtp) REVERT: F 430 MET cc_start: 0.8192 (tmm) cc_final: 0.7967 (tmm) REVERT: F 493 ASP cc_start: 0.8696 (m-30) cc_final: 0.8370 (t70) REVERT: G 242 SER cc_start: 0.8371 (m) cc_final: 0.7891 (t) REVERT: G 422 MET cc_start: 0.8457 (tpp) cc_final: 0.8200 (tpp) REVERT: H 281 MET cc_start: 0.2136 (mmp) cc_final: 0.1783 (mmp) outliers start: 61 outliers final: 55 residues processed: 321 average time/residue: 0.2017 time to fit residues: 107.2514 Evaluate side-chains 322 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 4 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 719 HIS C 206 ASN C 337 GLN D 225 GLN D 548 ASN G 478 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086028 restraints weight = 88421.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087976 restraints weight = 47102.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089297 restraints weight = 30454.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089173 restraints weight = 25786.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089159 restraints weight = 23634.185| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 34648 Z= 0.335 Angle : 0.774 15.775 46876 Z= 0.379 Chirality : 0.048 0.197 5269 Planarity : 0.005 0.054 6107 Dihedral : 7.368 141.825 4774 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.91 % Allowed : 12.91 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4259 helix: 1.36 (0.12), residues: 2074 sheet: -0.27 (0.21), residues: 593 loop : -0.03 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 717 TYR 0.025 0.002 TYR J 159 PHE 0.028 0.002 PHE B 275 TRP 0.029 0.002 TRP E 486 HIS 0.030 0.002 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.33 (34638) covalent geometry : angle 0.76929 / 0.38 (46870) hydrogen bonds : bond 0.04440 / 2.92 ( 1586) hydrogen bonds : angle 4.54351 / 3.26 ( 4503) metal coordination : bond 0.04553 / 1.92 ( 8) metal coordination : angle 7.38893 / 5.12 ( 6) Misc. bond : bond 0.00101 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7240 (ppp) cc_final: 0.5396 (mmt) REVERT: B 293 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 342 MET cc_start: 0.9126 (mtp) cc_final: 0.8388 (mtm) REVERT: B 348 ARG cc_start: 0.8246 (ptp90) cc_final: 0.7792 (ptp-170) REVERT: C 474 LEU cc_start: 0.8759 (mm) cc_final: 0.8364 (pp) REVERT: C 651 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: D 208 MET cc_start: 0.6264 (ppp) cc_final: 0.5873 (ppp) REVERT: D 342 MET cc_start: 0.9388 (tpp) cc_final: 0.9136 (tpp) REVERT: D 359 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.7685 (mtm-85) REVERT: D 556 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8074 (mp0) REVERT: E 254 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7770 (p90) REVERT: E 314 ASP cc_start: 0.8911 (t0) cc_final: 0.8485 (m-30) REVERT: E 332 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7756 (ttm-80) REVERT: E 342 MET cc_start: 0.8797 (mtp) cc_final: 0.8429 (mtp) REVERT: F 493 ASP cc_start: 0.8777 (m-30) cc_final: 0.8385 (t70) REVERT: G 122 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8134 (mm) REVERT: G 242 SER cc_start: 0.8574 (m) cc_final: 0.8193 (t) REVERT: G 344 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6700 (p90) REVERT: H 281 MET cc_start: 0.2288 (mmp) cc_final: 0.1915 (mmp) outliers start: 70 outliers final: 49 residues processed: 308 average time/residue: 0.2061 time to fit residues: 104.8647 Evaluate side-chains 298 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 624 LYS Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 575 ILE Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 253 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 254 ARG Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 329 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 157 optimal weight: 0.6980 chunk 389 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS C 719 HIS D 225 GLN D 548 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088139 restraints weight = 86615.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090497 restraints weight = 44529.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091532 restraints weight = 27730.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091750 restraints weight = 23651.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091744 restraints weight = 21552.089| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34648 Z= 0.121 Angle : 0.619 18.679 46876 Z= 0.294 Chirality : 0.042 0.191 5269 Planarity : 0.004 0.047 6107 Dihedral : 7.099 141.183 4774 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.37 % Allowed : 13.51 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4259 helix: 1.59 (0.12), residues: 2065 sheet: -0.10 (0.21), residues: 594 loop : 0.11 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 359 TYR 0.022 0.001 TYR G 445 PHE 0.018 0.001 PHE G 340 TRP 0.010 0.001 TRP E 486 HIS 0.003 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (34638) covalent geometry : angle 0.61570 / 0.29 (46870) hydrogen bonds : bond 0.03140 / 2.07 ( 1586) hydrogen bonds : angle 4.11153 / 2.95 ( 4503) metal coordination : bond 0.01478 / 0.62 ( 8) metal coordination : angle 5.50481 / 4.38 ( 6) Misc. bond : bond 0.00079 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6115.50 seconds wall clock time: 106 minutes 21.43 seconds (6381.43 seconds total)