Starting phenix.real_space_refine on Fri Mar 6 20:44:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8das_27274/03_2026/8das_27274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8das_27274/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8das_27274/03_2026/8das_27274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8das_27274/03_2026/8das_27274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8das_27274/03_2026/8das_27274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8das_27274/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 7.81, per 1000 atoms: 0.23 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 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: 1.28 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: 6.96 Time building geometry restraints manager: 4.40 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: 21002 28.56 - 57.11: 368 57.11 - 85.67: 40 85.67 - 114.22: 6 114.22 - 142.78: 9 Dihedral angle restraints: 21425 sinusoidal: 8954 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 21422 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.290 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 11.257 142.777 13351 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 covalent geometry : bond 0.00318 (34638) covalent geometry : angle 0.54734 (46870) hydrogen bonds : bond 0.14818 ( 1586) hydrogen bonds : angle 5.47046 ( 4503) metal coordination : bond 0.08341 ( 8) metal coordination : angle 2.62217 ( 6) Misc. bond : bond 0.62969 ( 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 : 1.269 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: 0.2447 time to fit residues: 228.7903 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 : 1.123 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 716 HIS B 206 ASN B 651 GLN 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 = 0.3962 r_free = 0.3962 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090357 restraints weight = 87474.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092881 restraints weight = 44135.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094092 restraints weight = 26525.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094150 restraints weight = 23088.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094141 restraints weight = 21008.270| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34648 Z= 0.138 Angle : 0.635 11.154 46876 Z= 0.310 Chirality : 0.044 0.174 5269 Planarity : 0.004 0.051 6107 Dihedral : 9.827 135.461 4969 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.97 % Allowed : 8.89 % Favored : 89.14 % 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 0.015 0.001 TYR G 439 PHE 0.021 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 covalent geometry : bond 0.00310 (34638) covalent geometry : angle 0.63401 (46870) hydrogen bonds : bond 0.03851 ( 1586) hydrogen bonds : angle 4.48807 ( 4503) metal coordination : bond 0.01408 ( 8) metal coordination : angle 2.85531 ( 6) Misc. bond : bond 0.00403 ( 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 : 1.300 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: 0.6958 (ppp) cc_final: 0.5281 (mmt) REVERT: A 314 ASP cc_start: 0.8684 (t0) cc_final: 0.8425 (t0) REVERT: A 359 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.8004 (mtp-110) REVERT: A 476 GLU cc_start: 0.7398 (pm20) cc_final: 0.7176 (pm20) REVERT: B 208 MET cc_start: 0.5558 (mmp) cc_final: 0.4815 (tpt) REVERT: B 342 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: B 348 ARG cc_start: 0.8266 (ptp90) cc_final: 0.7986 (ptp90) REVERT: B 574 ASP cc_start: 0.8606 (m-30) cc_final: 0.8348 (t0) REVERT: B 773 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7286 (mm-30) REVERT: B 774 LEU cc_start: 0.8712 (tp) cc_final: 0.8449 (tp) REVERT: C 96 ARG cc_start: 0.6972 (tpm170) cc_final: 0.6611 (mtp-110) REVERT: C 253 MET cc_start: 0.8221 (mtp) cc_final: 0.7875 (mtp) REVERT: C 348 ARG cc_start: 0.6821 (tpp-160) cc_final: 0.6301 (ptp-170) REVERT: C 474 LEU cc_start: 0.8781 (mm) cc_final: 0.8455 (pt) REVERT: D 208 MET cc_start: 0.6343 (ppp) cc_final: 0.5461 (tpt) REVERT: D 304 GLU cc_start: 0.8412 (tp30) cc_final: 0.8006 (mm-30) REVERT: D 359 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: D 514 THR cc_start: 0.8564 (m) cc_final: 0.8324 (p) REVERT: D 556 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8091 (mp0) REVERT: E 378 ASP cc_start: 0.8154 (t0) cc_final: 0.7890 (t0) REVERT: E 556 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8229 (mt-10) REVERT: E 635 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7580 (mmm160) REVERT: E 689 THR cc_start: 0.8648 (p) cc_final: 0.8406 (p) REVERT: F 223 MET cc_start: 0.8724 (tpp) cc_final: 0.8299 (tpp) REVERT: F 246 LYS cc_start: 0.8144 (tptp) cc_final: 0.7787 (tmtt) REVERT: F 315 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7671 (tp30) REVERT: F 556 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8069 (tp30) REVERT: F 762 MET cc_start: 0.8083 (ptm) cc_final: 0.7609 (ptm) REVERT: G 187 SER cc_start: 0.6988 (t) cc_final: 0.6736 (m) REVERT: G 242 SER cc_start: 0.8520 (m) cc_final: 0.8120 (p) REVERT: G 254 TYR cc_start: 0.7786 (t80) cc_final: 0.7328 (t80) REVERT: J 158 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6938 (p0) outliers start: 72 outliers final: 31 residues processed: 388 average time/residue: 0.2144 time to fit residues: 134.4238 Evaluate side-chains 320 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 665 SER Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain C residue 177 ASP 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 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 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: 0.5980 chunk 423 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 191 optimal weight: 0.0470 chunk 204 optimal weight: 0.9980 chunk 329 optimal weight: 0.7980 chunk 283 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN D 548 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091510 restraints weight = 86894.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093728 restraints weight = 44205.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094786 restraints weight = 29560.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095019 restraints weight = 22677.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095153 restraints weight = 22259.516| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2375 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= 0.118 Angle : 0.583 11.807 46876 Z= 0.282 Chirality : 0.042 0.234 5269 Planarity : 0.004 0.085 6107 Dihedral : 9.197 135.318 4939 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.67 % Allowed : 10.28 % Favored : 88.05 % 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: 1.46 (0.13), residues: 4259 helix: 1.89 (0.12), residues: 2069 sheet: -0.08 (0.21), residues: 594 loop : 0.27 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.015 0.001 TYR G 439 PHE 0.015 0.001 PHE G 340 TRP 0.011 0.001 TRP E 486 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00265 (34638) covalent geometry : angle 0.58149 (46870) hydrogen bonds : bond 0.03378 ( 1586) hydrogen bonds : angle 4.21871 ( 4503) metal coordination : bond 0.01991 ( 8) metal coordination : angle 3.21446 ( 6) Misc. bond : bond 0.00092 ( 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: 61 poor density : 307 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6866 (ppp) cc_final: 0.5261 (mmt) REVERT: A 359 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.8006 (mtp-110) REVERT: A 476 GLU cc_start: 0.7299 (pm20) cc_final: 0.7053 (pm20) REVERT: A 566 GLU cc_start: 0.7588 (mp0) cc_final: 0.7293 (mp0) REVERT: B 208 MET cc_start: 0.5732 (mmp) cc_final: 0.5101 (tpt) REVERT: B 215 ASP cc_start: 0.9112 (t0) cc_final: 0.8829 (t0) REVERT: B 285 MET cc_start: 0.8860 (mmm) cc_final: 0.8652 (mmt) REVERT: B 342 MET cc_start: 0.9036 (tpp) cc_final: 0.8258 (mtp) REVERT: B 574 ASP cc_start: 0.8600 (m-30) cc_final: 0.8340 (t0) REVERT: C 253 MET cc_start: 0.8192 (mtp) cc_final: 0.7851 (mtp) REVERT: C 474 LEU cc_start: 0.8730 (mm) cc_final: 0.8444 (pt) REVERT: C 651 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: D 304 GLU cc_start: 0.8435 (tp30) cc_final: 0.8043 (mm-30) REVERT: D 514 THR cc_start: 0.8551 (m) cc_final: 0.8313 (p) REVERT: D 556 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8061 (mp0) REVERT: D 784 MET cc_start: 0.8612 (mmm) cc_final: 0.8150 (mmm) REVERT: E 285 MET cc_start: 0.8567 (mmm) cc_final: 0.8307 (mmm) REVERT: E 314 ASP cc_start: 0.8835 (t0) cc_final: 0.8363 (m-30) REVERT: E 342 MET cc_start: 0.8755 (mtp) cc_final: 0.8489 (mtp) REVERT: E 556 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8278 (mt-10) REVERT: F 223 MET cc_start: 0.8698 (tpp) cc_final: 0.8266 (tpp) REVERT: F 246 LYS cc_start: 0.8168 (tptp) cc_final: 0.7890 (tmtt) REVERT: F 315 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7682 (tp30) REVERT: F 762 MET cc_start: 0.8014 (ptm) cc_final: 0.7533 (ptm) REVERT: F 782 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8828 (tm-30) REVERT: G 242 SER cc_start: 0.8511 (m) cc_final: 0.8045 (p) REVERT: G 254 TYR cc_start: 0.7733 (t80) cc_final: 0.7292 (t80) REVERT: H 238 MET cc_start: 0.8077 (ttm) cc_final: 0.7670 (tpp) outliers start: 61 outliers final: 36 residues processed: 355 average time/residue: 0.2042 time to fit residues: 119.5302 Evaluate side-chains 304 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 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 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 644 LEU 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 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 504 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 237 SER 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 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: 0.5980 chunk 360 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 719 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.121010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090924 restraints weight = 86669.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.093849 restraints weight = 43205.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094719 restraints weight = 26032.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094812 restraints weight = 23463.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094925 restraints weight = 21145.422| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34648 Z= 0.121 Angle : 0.572 12.924 46876 Z= 0.273 Chirality : 0.042 0.171 5269 Planarity : 0.004 0.052 6107 Dihedral : 8.898 136.184 4934 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.08 % Allowed : 10.64 % Favored : 87.28 % 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: 1.86 (0.12), residues: 2068 sheet: -0.02 (0.21), residues: 586 loop : 0.27 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 359 TYR 0.016 0.001 TYR G 439 PHE 0.027 0.001 PHE E 585 TRP 0.010 0.001 TRP E 486 HIS 0.021 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00278 (34638) covalent geometry : angle 0.57067 (46870) hydrogen bonds : bond 0.03179 ( 1586) hydrogen bonds : angle 4.12454 ( 4503) metal coordination : bond 0.02224 ( 8) metal coordination : angle 3.43624 ( 6) Misc. bond : bond 0.00075 ( 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: 76 poor density : 281 time to evaluate : 1.290 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: 0.5253 (mmt) REVERT: A 359 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.8006 (mtp-110) REVERT: A 566 GLU cc_start: 0.7565 (mp0) cc_final: 0.7228 (mp0) REVERT: B 208 MET cc_start: 0.5759 (mmp) cc_final: 0.5110 (tpt) REVERT: B 215 ASP cc_start: 0.9111 (t0) cc_final: 0.8824 (t0) REVERT: B 342 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: B 574 ASP cc_start: 0.8606 (m-30) cc_final: 0.8353 (t0) REVERT: C 253 MET cc_start: 0.8262 (mtp) cc_final: 0.7925 (mtp) REVERT: C 398 MET cc_start: 0.8414 (mtt) cc_final: 0.8163 (mtt) REVERT: C 474 LEU cc_start: 0.8697 (mm) cc_final: 0.8364 (pp) REVERT: C 651 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: D 208 MET cc_start: 0.6217 (ppp) cc_final: 0.5305 (tpt) REVERT: D 223 MET cc_start: 0.8623 (mmm) cc_final: 0.8411 (tpp) REVERT: D 304 GLU cc_start: 0.8388 (tp30) cc_final: 0.8010 (mm-30) REVERT: D 359 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: D 514 THR cc_start: 0.8569 (m) cc_final: 0.8339 (p) REVERT: D 556 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8081 (mp0) REVERT: E 314 ASP cc_start: 0.8811 (t0) cc_final: 0.8319 (m-30) REVERT: E 342 MET cc_start: 0.8769 (mtp) cc_final: 0.8464 (mtp) REVERT: E 556 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8215 (mt-10) REVERT: E 635 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7704 (mmm160) REVERT: F 246 LYS cc_start: 0.8122 (tptp) cc_final: 0.7896 (tmtt) REVERT: F 315 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7692 (tp30) REVERT: F 762 MET cc_start: 0.8012 (ptm) cc_final: 0.7621 (ptm) REVERT: G 242 SER cc_start: 0.8444 (m) cc_final: 0.7947 (t) REVERT: G 254 TYR cc_start: 0.7787 (t80) cc_final: 0.7371 (t80) REVERT: G 344 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7470 (p90) REVERT: H 238 MET cc_start: 0.8248 (ttm) cc_final: 0.7719 (tpp) outliers start: 76 outliers final: 41 residues processed: 340 average time/residue: 0.1992 time to fit residues: 111.6699 Evaluate side-chains 310 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 MET 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 214 ASP 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 278 LEU 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 298 MET 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 495 MET 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 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: 0.5980 chunk 363 optimal weight: 0.8980 chunk 260 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 412 optimal weight: 0.0570 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 145 optimal weight: 0.8980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 716 HIS B 206 ASN C 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092183 restraints weight = 86493.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095026 restraints weight = 45024.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095924 restraints weight = 27401.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095971 restraints weight = 23425.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096082 restraints weight = 21240.223| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34648 Z= 0.101 Angle : 0.559 13.674 46876 Z= 0.266 Chirality : 0.042 0.229 5269 Planarity : 0.003 0.049 6107 Dihedral : 8.548 136.002 4931 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.19 % Allowed : 10.99 % Favored : 86.82 % 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: 1.47 (0.13), residues: 4259 helix: 1.86 (0.12), residues: 2070 sheet: 0.08 (0.21), residues: 589 loop : 0.29 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 359 TYR 0.016 0.001 TYR G 439 PHE 0.024 0.001 PHE G 340 TRP 0.008 0.001 TRP E 486 HIS 0.011 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00221 (34638) covalent geometry : angle 0.55856 (46870) hydrogen bonds : bond 0.02891 ( 1586) hydrogen bonds : angle 3.99130 ( 4503) metal coordination : bond 0.01592 ( 8) metal coordination : angle 2.90384 ( 6) Misc. bond : bond 0.00082 ( 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 380 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 300 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6877 (ppp) cc_final: 0.5238 (mmt) REVERT: A 359 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7990 (mtp-110) REVERT: A 566 GLU cc_start: 0.7682 (mp0) cc_final: 0.7341 (mp0) REVERT: A 618 MET cc_start: 0.8869 (ttp) cc_final: 0.8663 (ttp) REVERT: B 208 MET cc_start: 0.5717 (mmp) cc_final: 0.5130 (tpt) REVERT: B 342 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8292 (mtp) REVERT: B 348 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7778 (ptt180) REVERT: B 574 ASP cc_start: 0.8537 (m-30) cc_final: 0.8310 (t0) REVERT: C 474 LEU cc_start: 0.8694 (mm) cc_final: 0.8296 (pp) REVERT: D 208 MET cc_start: 0.6160 (ppp) cc_final: 0.5229 (tpt) REVERT: D 223 MET cc_start: 0.8617 (mmm) cc_final: 0.8383 (tpp) REVERT: D 304 GLU cc_start: 0.8372 (tp30) cc_final: 0.8000 (mm-30) REVERT: D 342 MET cc_start: 0.9256 (tpp) cc_final: 0.8990 (tpp) REVERT: D 514 THR cc_start: 0.8551 (m) cc_final: 0.8318 (p) REVERT: D 556 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8025 (mp0) REVERT: E 223 MET cc_start: 0.8379 (tpp) cc_final: 0.8151 (mmm) REVERT: E 314 ASP cc_start: 0.8763 (t0) cc_final: 0.8252 (m-30) REVERT: E 342 MET cc_start: 0.8751 (mtp) cc_final: 0.8414 (mtp) REVERT: E 556 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8221 (mt-10) REVERT: F 246 LYS cc_start: 0.8126 (tptp) cc_final: 0.7888 (tmtt) REVERT: F 315 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7670 (tp30) REVERT: F 343 ASP cc_start: 0.8306 (m-30) cc_final: 0.8020 (m-30) REVERT: F 493 ASP cc_start: 0.8713 (m-30) cc_final: 0.8379 (t70) REVERT: F 762 MET cc_start: 0.7922 (ptm) cc_final: 0.7487 (ptm) REVERT: F 785 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8107 (tptt) REVERT: G 242 SER cc_start: 0.8389 (m) cc_final: 0.7880 (t) REVERT: G 254 TYR cc_start: 0.7712 (t80) cc_final: 0.7316 (t80) REVERT: G 344 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.6790 (p90) REVERT: K 201 MET cc_start: 0.1270 (ttm) cc_final: 0.0907 (ptm) outliers start: 80 outliers final: 48 residues processed: 362 average time/residue: 0.2010 time to fit residues: 120.1412 Evaluate side-chains 325 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU 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 536 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 342 MET 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 C residue 177 ASP Chi-restraints excluded: chain C residue 404 VAL 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 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 335 VAL Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain E residue 441 ASP 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 F residue 785 LYS 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 383 THR Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET 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 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: 4.9990 chunk 335 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 403 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091255 restraints weight = 86573.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093682 restraints weight = 45238.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094280 restraints weight = 29859.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094668 restraints weight = 24010.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094608 restraints weight = 22209.024| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34648 Z= 0.126 Angle : 0.572 14.593 46876 Z= 0.271 Chirality : 0.042 0.169 5269 Planarity : 0.003 0.049 6107 Dihedral : 8.405 136.567 4931 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.86 % Allowed : 11.84 % Favored : 86.30 % 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: 1.47 (0.13), residues: 4259 helix: 1.86 (0.12), residues: 2071 sheet: 0.11 (0.21), residues: 587 loop : 0.28 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 359 TYR 0.017 0.001 TYR G 439 PHE 0.025 0.001 PHE G 340 TRP 0.011 0.001 TRP E 486 HIS 0.003 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00293 (34638) covalent geometry : angle 0.57038 (46870) hydrogen bonds : bond 0.02999 ( 1586) hydrogen bonds : angle 3.98066 ( 4503) metal coordination : bond 0.02309 ( 8) metal coordination : angle 3.36192 ( 6) Misc. bond : bond 0.00082 ( 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 349 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6958 (ppp) cc_final: 0.5216 (mmt) REVERT: A 331 GLU cc_start: 0.6938 (pt0) cc_final: 0.6532 (pt0) REVERT: A 359 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7984 (mtp-110) REVERT: A 566 GLU cc_start: 0.7685 (mp0) cc_final: 0.7367 (mp0) REVERT: B 246 LYS cc_start: 0.8871 (mmpt) cc_final: 0.8618 (mmmt) REVERT: B 285 MET cc_start: 0.8763 (mmm) cc_final: 0.8560 (mmt) REVERT: B 342 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8409 (mtp) REVERT: B 348 ARG cc_start: 0.8289 (ptp90) cc_final: 0.7650 (ptp90) REVERT: B 574 ASP cc_start: 0.8560 (m-30) cc_final: 0.8282 (t0) REVERT: C 474 LEU cc_start: 0.8679 (mm) cc_final: 0.8272 (pp) REVERT: C 651 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: D 208 MET cc_start: 0.6158 (ppp) cc_final: 0.5160 (tpt) REVERT: D 223 MET cc_start: 0.8621 (mmm) cc_final: 0.8370 (tpp) REVERT: D 304 GLU cc_start: 0.8405 (tp30) cc_final: 0.8048 (mm-30) REVERT: D 359 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7616 (mtm-85) REVERT: D 514 THR cc_start: 0.8581 (m) cc_final: 0.8349 (p) REVERT: D 556 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8056 (mp0) REVERT: E 331 GLU cc_start: 0.8215 (mp0) cc_final: 0.7903 (pm20) REVERT: E 332 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7463 (ttm-80) REVERT: E 342 MET cc_start: 0.8755 (mtp) cc_final: 0.8389 (mtp) REVERT: E 430 MET cc_start: 0.9309 (tpp) cc_final: 0.9079 (tpp) REVERT: E 556 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8213 (mt-10) REVERT: E 635 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7684 (mmm160) REVERT: F 246 LYS cc_start: 0.8098 (tptp) cc_final: 0.7885 (tmtt) REVERT: F 315 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7701 (tp30) REVERT: F 343 ASP cc_start: 0.8353 (m-30) cc_final: 0.8072 (m-30) REVERT: F 493 ASP cc_start: 0.8690 (m-30) cc_final: 0.8359 (t70) REVERT: F 762 MET cc_start: 0.7914 (ptm) cc_final: 0.7433 (ptm) REVERT: F 785 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8145 (tptt) REVERT: G 242 SER cc_start: 0.8404 (m) cc_final: 0.7922 (t) REVERT: G 422 MET cc_start: 0.8323 (tpp) cc_final: 0.8110 (mmm) REVERT: K 201 MET cc_start: 0.1279 (ttm) cc_final: 0.0911 (ptm) outliers start: 68 outliers final: 48 residues processed: 334 average time/residue: 0.2068 time to fit residues: 112.8433 Evaluate side-chains 320 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 643 ILE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 342 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 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 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 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 E residue 635 ARG 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 F residue 785 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 231 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 324 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 318 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090926 restraints weight = 86996.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093876 restraints weight = 43084.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094369 restraints weight = 26288.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094667 restraints weight = 23812.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094793 restraints weight = 21863.336| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34648 Z= 0.129 Angle : 0.577 15.566 46876 Z= 0.275 Chirality : 0.042 0.207 5269 Planarity : 0.004 0.050 6107 Dihedral : 8.325 136.706 4929 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.02 % Allowed : 11.92 % Favored : 86.05 % 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: 1.45 (0.13), residues: 4259 helix: 1.84 (0.12), residues: 2071 sheet: 0.08 (0.21), residues: 592 loop : 0.27 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 359 TYR 0.016 0.001 TYR G 439 PHE 0.024 0.001 PHE G 340 TRP 0.011 0.001 TRP E 486 HIS 0.013 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00301 (34638) covalent geometry : angle 0.57600 (46870) hydrogen bonds : bond 0.02999 ( 1586) hydrogen bonds : angle 3.97278 ( 4503) metal coordination : bond 0.02419 ( 8) metal coordination : angle 3.58779 ( 6) Misc. bond : bond 0.00080 ( 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 348 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 274 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6886 (ppp) cc_final: 0.5083 (mmt) REVERT: A 331 GLU cc_start: 0.7037 (pt0) cc_final: 0.6685 (pt0) REVERT: A 359 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7960 (mtp-110) REVERT: A 566 GLU cc_start: 0.7726 (mp0) cc_final: 0.7425 (mp0) REVERT: B 246 LYS cc_start: 0.8891 (mmpt) cc_final: 0.8627 (mmmt) REVERT: B 342 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: B 574 ASP cc_start: 0.8597 (m-30) cc_final: 0.8366 (t0) REVERT: C 464 PHE cc_start: 0.8573 (t80) cc_final: 0.8349 (t80) REVERT: C 474 LEU cc_start: 0.8685 (mm) cc_final: 0.8262 (pp) REVERT: C 651 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: D 208 MET cc_start: 0.6160 (ppp) cc_final: 0.5843 (ppp) REVERT: D 223 MET cc_start: 0.8625 (mmm) cc_final: 0.8387 (tpp) REVERT: D 304 GLU cc_start: 0.8444 (tp30) cc_final: 0.8058 (mm-30) REVERT: D 342 MET cc_start: 0.9348 (tpp) cc_final: 0.8985 (tpp) REVERT: D 359 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: D 514 THR cc_start: 0.8583 (m) cc_final: 0.8335 (p) REVERT: D 556 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8019 (mp0) REVERT: E 223 MET cc_start: 0.8452 (tpp) cc_final: 0.8217 (mmm) REVERT: E 314 ASP cc_start: 0.8791 (t0) cc_final: 0.8360 (m-30) REVERT: E 331 GLU cc_start: 0.8235 (mp0) cc_final: 0.7843 (pm20) REVERT: E 332 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7442 (ttm-80) REVERT: E 342 MET cc_start: 0.8773 (mtp) cc_final: 0.8389 (mtp) REVERT: E 556 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8207 (mt-10) REVERT: E 560 MET cc_start: 0.8126 (mpp) cc_final: 0.7907 (mmm) REVERT: E 635 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7677 (mmm160) REVERT: F 315 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7713 (tp30) REVERT: F 493 ASP cc_start: 0.8705 (m-30) cc_final: 0.8366 (t70) REVERT: F 762 MET cc_start: 0.7904 (ptm) cc_final: 0.7418 (ptm) REVERT: F 785 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (tptt) REVERT: G 242 SER cc_start: 0.8455 (m) cc_final: 0.7969 (t) REVERT: G 344 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6787 (p90) REVERT: K 201 MET cc_start: 0.1431 (ttm) cc_final: 0.1065 (ptm) outliers start: 74 outliers final: 51 residues processed: 334 average time/residue: 0.2089 time to fit residues: 114.7601 Evaluate side-chains 324 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 B residue 253 MET Chi-restraints excluded: chain B residue 342 MET 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 C residue 177 ASP Chi-restraints excluded: chain C residue 404 VAL 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 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 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 E residue 635 ARG 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 F residue 785 LYS 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 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: 0.4980 chunk 221 optimal weight: 3.9990 chunk 378 optimal weight: 0.7980 chunk 22 optimal weight: 0.0060 chunk 191 optimal weight: 0.6980 chunk 424 optimal weight: 0.2980 chunk 307 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 420 optimal weight: 7.9990 chunk 411 optimal weight: 0.0050 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN F 295 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092694 restraints weight = 86552.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095608 restraints weight = 42656.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096677 restraints weight = 25248.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096677 restraints weight = 22666.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096694 restraints weight = 20458.228| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34648 Z= 0.098 Angle : 0.570 16.090 46876 Z= 0.269 Chirality : 0.042 0.200 5269 Planarity : 0.003 0.048 6107 Dihedral : 8.148 138.548 4929 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.56 % Allowed : 12.47 % Favored : 85.97 % 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: 1.46 (0.13), residues: 4259 helix: 1.83 (0.12), residues: 2070 sheet: 0.24 (0.21), residues: 584 loop : 0.23 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 359 TYR 0.030 0.001 TYR G 445 PHE 0.021 0.001 PHE G 340 TRP 0.009 0.001 TRP B 561 HIS 0.005 0.000 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00211 (34638) covalent geometry : angle 0.56908 (46870) hydrogen bonds : bond 0.02638 ( 1586) hydrogen bonds : angle 3.86210 ( 4503) metal coordination : bond 0.01379 ( 8) metal coordination : angle 2.93934 ( 6) Misc. bond : bond 0.00078 ( 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 345 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6857 (ppp) cc_final: 0.5092 (mmt) REVERT: A 331 GLU cc_start: 0.7056 (pt0) cc_final: 0.6542 (pt0) REVERT: A 359 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7992 (mtp-110) REVERT: B 246 LYS cc_start: 0.8891 (mmpt) cc_final: 0.8629 (mmmt) REVERT: B 342 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: B 348 ARG cc_start: 0.8167 (ptp90) cc_final: 0.7906 (ptp-170) REVERT: B 574 ASP cc_start: 0.8521 (m-30) cc_final: 0.8269 (t0) REVERT: C 464 PHE cc_start: 0.8481 (t80) cc_final: 0.8225 (t80) REVERT: C 474 LEU cc_start: 0.8674 (mm) cc_final: 0.8254 (pp) REVERT: C 651 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: D 208 MET cc_start: 0.6204 (ppp) cc_final: 0.5319 (tpt) REVERT: D 223 MET cc_start: 0.8602 (mmm) cc_final: 0.8330 (tpp) REVERT: D 304 GLU cc_start: 0.8294 (tp30) cc_final: 0.7936 (mm-30) REVERT: D 323 ARG cc_start: 0.7531 (tmt170) cc_final: 0.7133 (tmt170) REVERT: D 342 MET cc_start: 0.9330 (tpp) cc_final: 0.8970 (tpp) REVERT: D 359 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7661 (mtm-85) REVERT: D 514 THR cc_start: 0.8570 (m) cc_final: 0.8341 (p) REVERT: D 556 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8041 (mp0) REVERT: E 314 ASP cc_start: 0.8640 (t0) cc_final: 0.8249 (m-30) REVERT: E 342 MET cc_start: 0.8722 (mtp) cc_final: 0.8270 (mtp) REVERT: E 556 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8175 (mt-10) REVERT: F 345 MET cc_start: 0.8317 (tpp) cc_final: 0.8058 (tpp) REVERT: F 430 MET cc_start: 0.8158 (tmm) cc_final: 0.7907 (tmm) REVERT: F 493 ASP cc_start: 0.8687 (m-30) cc_final: 0.8369 (t70) REVERT: F 762 MET cc_start: 0.7891 (ptm) cc_final: 0.7436 (ptm) REVERT: F 785 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8175 (tptp) REVERT: G 242 SER cc_start: 0.8347 (m) cc_final: 0.7868 (t) REVERT: G 440 MET cc_start: 0.8416 (ttt) cc_final: 0.8210 (mtt) REVERT: K 201 MET cc_start: 0.1336 (ttm) cc_final: 0.0951 (ptm) outliers start: 57 outliers final: 44 residues processed: 332 average time/residue: 0.2001 time to fit residues: 110.4127 Evaluate side-chains 313 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU 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 B residue 253 MET Chi-restraints excluded: chain B residue 342 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 C residue 177 ASP Chi-restraints excluded: chain C residue 404 VAL 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 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 752 TYR 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 474 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 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 382 VAL 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 237 SER 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 305 MET Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 226 VAL 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: 0.0570 chunk 127 optimal weight: 30.0000 chunk 336 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 331 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.122031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091710 restraints weight = 86649.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094056 restraints weight = 44045.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095036 restraints weight = 29550.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095273 restraints weight = 23281.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095596 restraints weight = 22016.082| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 34648 Z= 0.108 Angle : 0.577 17.398 46876 Z= 0.272 Chirality : 0.042 0.204 5269 Planarity : 0.003 0.049 6107 Dihedral : 8.074 141.107 4927 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.56 % Allowed : 12.77 % Favored : 85.67 % 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: 1.46 (0.13), residues: 4259 helix: 1.81 (0.12), residues: 2071 sheet: 0.29 (0.21), residues: 583 loop : 0.23 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 359 TYR 0.021 0.001 TYR G 445 PHE 0.013 0.001 PHE A 144 TRP 0.010 0.001 TRP E 486 HIS 0.003 0.000 HIS G 521 Details of bonding type rmsd covalent geometry : bond 0.00246 (34638) covalent geometry : angle 0.57634 (46870) hydrogen bonds : bond 0.02747 ( 1586) hydrogen bonds : angle 3.86982 ( 4503) metal coordination : bond 0.01836 ( 8) metal coordination : angle 3.05931 ( 6) Misc. bond : bond 0.00080 ( 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 325 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6932 (ppp) cc_final: 0.5145 (mmt) REVERT: A 331 GLU cc_start: 0.7067 (pt0) cc_final: 0.6745 (pt0) REVERT: A 359 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.8010 (mtp-110) REVERT: B 208 MET cc_start: 0.5182 (mmp) cc_final: 0.4654 (ttt) REVERT: B 246 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8634 (mmmt) REVERT: B 293 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 342 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8338 (mtp) REVERT: B 348 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7852 (ptp-170) REVERT: B 574 ASP cc_start: 0.8567 (m-30) cc_final: 0.8312 (t0) REVERT: C 464 PHE cc_start: 0.8442 (t80) cc_final: 0.8170 (t80) REVERT: C 474 LEU cc_start: 0.8696 (mm) cc_final: 0.8252 (pp) REVERT: C 651 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: D 208 MET cc_start: 0.6245 (ppp) cc_final: 0.5985 (ppp) REVERT: D 223 MET cc_start: 0.8642 (mmm) cc_final: 0.8377 (tpp) REVERT: D 304 GLU cc_start: 0.8379 (tp30) cc_final: 0.8010 (mm-30) REVERT: D 323 ARG cc_start: 0.7573 (tmt170) cc_final: 0.7213 (tmt170) REVERT: D 342 MET cc_start: 0.9343 (tpp) cc_final: 0.9046 (tpp) REVERT: D 359 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: D 514 THR cc_start: 0.8584 (m) cc_final: 0.8354 (p) REVERT: D 556 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8030 (mp0) REVERT: E 229 MET cc_start: 0.8944 (tpt) cc_final: 0.8495 (tpt) REVERT: E 314 ASP cc_start: 0.8636 (t0) cc_final: 0.8251 (m-30) REVERT: E 331 GLU cc_start: 0.8213 (mp0) cc_final: 0.7894 (pm20) REVERT: E 332 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7453 (ttm-80) REVERT: E 342 MET cc_start: 0.8723 (mtp) cc_final: 0.8272 (mtp) REVERT: E 556 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8114 (mt-10) REVERT: F 345 MET cc_start: 0.8296 (tpp) cc_final: 0.8086 (tpp) REVERT: F 430 MET cc_start: 0.8127 (tmm) cc_final: 0.7879 (tmm) REVERT: F 493 ASP cc_start: 0.8682 (m-30) cc_final: 0.8358 (t70) REVERT: F 762 MET cc_start: 0.7899 (ptm) cc_final: 0.7441 (ptm) REVERT: F 785 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8101 (tppt) REVERT: G 242 SER cc_start: 0.8359 (m) cc_final: 0.7876 (t) REVERT: G 422 MET cc_start: 0.8438 (tpp) cc_final: 0.8217 (tpp) REVERT: K 201 MET cc_start: 0.1392 (ttm) cc_final: 0.1009 (ptm) outliers start: 57 outliers final: 44 residues processed: 315 average time/residue: 0.2094 time to fit residues: 109.0114 Evaluate side-chains 312 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU 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 643 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 342 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 C residue 177 ASP Chi-restraints excluded: chain C residue 404 VAL 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 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 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 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 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 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 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 166 THR Chi-restraints excluded: chain K residue 226 VAL 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: 7.9990 chunk 164 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 394 HIS C 719 HIS D 225 GLN F 295 ASN G 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.117940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087500 restraints weight = 88114.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089542 restraints weight = 46329.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.091251 restraints weight = 29930.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091048 restraints weight = 24250.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090937 restraints weight = 21803.169| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 34648 Z= 0.222 Angle : 0.677 14.986 46876 Z= 0.326 Chirality : 0.045 0.186 5269 Planarity : 0.004 0.052 6107 Dihedral : 8.335 142.814 4927 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.75 % Allowed : 12.66 % 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: 1.19 (0.13), residues: 4259 helix: 1.62 (0.12), residues: 2069 sheet: -0.02 (0.21), residues: 595 loop : 0.14 (0.17), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 463 TYR 0.020 0.001 TYR G 439 PHE 0.019 0.002 PHE A 144 TRP 0.023 0.002 TRP E 486 HIS 0.006 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00527 (34638) covalent geometry : angle 0.67404 (46870) hydrogen bonds : bond 0.03770 ( 1586) hydrogen bonds : angle 4.23079 ( 4503) metal coordination : bond 0.03588 ( 8) metal coordination : angle 5.74474 ( 6) Misc. bond : bond 0.00095 ( 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 328 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7062 (ppp) cc_final: 0.5289 (mmt) REVERT: A 359 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8042 (mtp-110) REVERT: B 208 MET cc_start: 0.5133 (mmp) cc_final: 0.4726 (ttt) REVERT: B 293 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: B 574 ASP cc_start: 0.8700 (m-30) cc_final: 0.8465 (t0) REVERT: C 464 PHE cc_start: 0.8595 (t80) cc_final: 0.8379 (t80) REVERT: C 474 LEU cc_start: 0.8754 (mm) cc_final: 0.8306 (pp) REVERT: C 651 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: D 208 MET cc_start: 0.6249 (ppp) cc_final: 0.5879 (ppp) REVERT: D 342 MET cc_start: 0.9361 (tpp) cc_final: 0.9101 (tpp) REVERT: D 359 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: D 556 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8038 (mp0) REVERT: E 229 MET cc_start: 0.8952 (tpt) cc_final: 0.8573 (tpt) REVERT: E 314 ASP cc_start: 0.8756 (t0) cc_final: 0.8327 (m-30) REVERT: E 331 GLU cc_start: 0.8251 (mp0) cc_final: 0.7842 (pm20) REVERT: E 332 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7441 (ttm-80) REVERT: E 342 MET cc_start: 0.8754 (mtp) cc_final: 0.8276 (mtp) REVERT: E 556 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8167 (mt-10) REVERT: F 345 MET cc_start: 0.8382 (tpp) cc_final: 0.8119 (tpp) REVERT: F 493 ASP cc_start: 0.8747 (m-30) cc_final: 0.8373 (t70) REVERT: F 785 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7961 (tppt) REVERT: G 242 SER cc_start: 0.8505 (m) cc_final: 0.7973 (t) REVERT: G 344 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.6668 (p90) REVERT: H 281 MET cc_start: 0.2321 (mmp) cc_final: 0.1960 (mmp) outliers start: 64 outliers final: 43 residues processed: 315 average time/residue: 0.2085 time to fit residues: 108.5027 Evaluate side-chains 304 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 452 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 404 VAL 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 719 HIS 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 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 524 VAL Chi-restraints excluded: chain F residue 719 HIS Chi-restraints excluded: chain F residue 785 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 344 HIS Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 495 MET 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 226 VAL 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: 1.9990 chunk 54 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 389 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.119306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088750 restraints weight = 87016.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090641 restraints weight = 45473.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091870 restraints weight = 30567.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091979 restraints weight = 24434.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092289 restraints weight = 22510.974| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34648 Z= 0.125 Angle : 0.610 16.530 46876 Z= 0.290 Chirality : 0.042 0.197 5269 Planarity : 0.004 0.049 6107 Dihedral : 8.220 142.052 4927 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.29 % Allowed : 13.29 % Favored : 85.43 % 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: 1.25 (0.13), residues: 4259 helix: 1.67 (0.12), residues: 2055 sheet: 0.06 (0.21), residues: 593 loop : 0.17 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 359 TYR 0.019 0.001 TYR G 445 PHE 0.021 0.001 PHE G 340 TRP 0.011 0.001 TRP E 486 HIS 0.012 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00288 (34638) covalent geometry : angle 0.60713 (46870) hydrogen bonds : bond 0.03110 ( 1586) hydrogen bonds : angle 4.04950 ( 4503) metal coordination : bond 0.02106 ( 8) metal coordination : angle 5.20823 ( 6) Misc. bond : bond 0.00082 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5950.75 seconds wall clock time: 103 minutes 19.28 seconds (6199.28 seconds total)