Starting phenix.real_space_refine on Fri Mar 6 22:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.map" model { file = "/net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dat_27275/03_2026/8dat_27275.cif" } resolution = 3.8 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= -0.022 sd= 1.089 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 157 5.16 5 C 21678 2.51 5 N 6018 2.21 5 O 6751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 34635 Number of models: 1 Model: "" Number of chains: 18 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: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4361 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} 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: "L" 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 28493 SG CYS G 137 46.570 46.552 94.504 1.00 85.59 S ATOM 28553 SG CYS G 145 50.237 47.200 94.103 1.00 76.33 S ATOM 28580 SG CYS G 148 48.689 46.859 97.510 1.00 77.07 S ATOM 29050 SG CYS G 204 76.186 88.657 113.339 1.00100.27 S ATOM 29148 SG CYS G 216 76.282 90.588 110.164 1.00 82.25 S ATOM 29169 SG CYS G 219 73.577 91.235 112.527 1.00 80.75 S Time building chain proxies: 7.74, per 1000 atoms: 0.22 Number of scatterers: 34635 At special positions: 0 Unit cell: (151.088, 167.048, 190.456, 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 157 16.00 P 29 15.00 O 6751 8.00 N 6018 7.00 C 21678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8210 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 25 sheets defined 52.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 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: 4.003A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.006A 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 202 through 207 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.521A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.333A 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: 3.790A 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 320 removed outlier: 4.131A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.141A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.047A 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 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.275A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 4.098A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.763A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 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: 3.625A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 764 " --> pdb=" O GLU A 760 " (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: 4.092A 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: 3.810A pdb=" N LYS B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 293 through 306 Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.207A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.979A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.631A 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 454 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.496A 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: 3.787A 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 589 through 592 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 671 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 763 removed outlier: 3.613A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 787 Processing helix chain 'C' and resid 52 through 60 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: 4.216A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.790A 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: 4.596A 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 removed outlier: 3.539A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.604A 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 315 through 319 Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.927A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.316A 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 Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.582A pdb=" N GLU C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.721A 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: 3.680A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.618A 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: 3.583A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 788 Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.637A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.125A 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 286 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 328 through 346 removed outlier: 4.238A 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: 4.039A 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: 3.938A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.600A 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 620 Processing helix chain 'D' and resid 640 through 645 removed outlier: 3.533A pdb=" N ARG D 645 " --> pdb=" O ALA D 642 " (cutoff:3.500A) 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: 3.757A 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: 4.210A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 244 removed outlier: 3.687A pdb=" N LYS E 241 " --> pdb=" O PRO E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.632A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.016A pdb=" N ILE E 319 " --> pdb=" O GLU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.914A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 472 through 476 removed outlier: 3.625A pdb=" N GLU E 476 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.211A 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: 3.729A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.537A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 592 Processing helix chain 'E' and resid 609 through 620 Processing helix chain 'E' and resid 635 through 639 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 Processing helix chain 'E' and resid 682 through 689 Processing helix chain 'E' and resid 693 through 719 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.679A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 4.655A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 237 through 244 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 328 through 345 removed outlier: 3.581A pdb=" N ARG F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) 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: 3.624A 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 Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.030A 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: 4.055A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 640 through 645 removed outlier: 3.575A pdb=" N ARG F 645 " --> pdb=" O ALA F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 671 Processing helix chain 'F' and resid 682 through 688 Processing helix chain 'F' and resid 693 through 719 Processing helix chain 'F' and resid 754 through 763 Processing helix chain 'F' and resid 770 through 788 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.647A 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 241 through 256 removed outlier: 4.327A pdb=" N ILE G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.820A 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 411 removed outlier: 4.097A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.750A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 525 removed outlier: 4.133A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.711A 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 Processing helix chain 'H' and resid 243 through 253 Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.905A pdb=" N VAL J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 160 removed outlier: 4.421A pdb=" N TYR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.797A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 260 Processing helix chain 'L' and resid 322 through 335 removed outlier: 3.763A pdb=" N VAL L 326 " --> pdb=" O THR L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 7.735A pdb=" N CYS A 92 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU A 37 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 94 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP A 39 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 6.841A pdb=" N LYS A 119 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 6.085A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.550A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 552 removed outlier: 6.933A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.350A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE G 215 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 278 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.632A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA9, 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: 5.768A pdb=" N VAL C 175 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU C 127 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 124 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.088A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 356 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 548 through 552 removed outlier: 7.074A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.818A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 479 through 480 removed outlier: 3.830A pdb=" N PHE D 549 " --> pdb=" O GLU D 480 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY D 523 " --> pdb=" O GLN D 651 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.693A pdb=" N ARG E 375 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 479 through 480 Processing sheet with id=AB8, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.954A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY F 250 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL F 377 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 548 through 552 removed outlier: 6.825A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.027A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 236 through 239 removed outlier: 3.939A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE G 396 " --> pdb=" O HIS G 468 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS G 468 " --> pdb=" O ILE G 396 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER G 398 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 466 " --> pdb=" O SER G 398 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AC4, first strand: chain 'G' and resid 415 through 416 removed outlier: 3.543A 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 115 removed outlier: 6.624A pdb=" N PHE J 104 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU J 169 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS J 106 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LEU J 171 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 216 removed outlier: 3.935A pdb=" N SER K 265 " --> pdb=" O GLN K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 312 through 316 removed outlier: 4.230A pdb=" N SER L 365 " --> pdb=" O GLN L 302 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU L 343 " --> pdb=" O LEU L 350 " (cutoff:3.500A) 1622 hydrogen bonds defined for protein. 4602 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: 6.94 Time building geometry restraints manager: 3.73 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: 11722 1.34 - 1.46: 6664 1.46 - 1.58: 16497 1.58 - 1.69: 46 1.69 - 1.81: 290 Bond restraints: 35219 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP 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 2.97e+01 bond pdb=" C5 ADP A 902 " pdb=" C6 ADP A 902 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+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 1.82e+01 ... (remaining 35214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 47224 2.30 - 4.60: 342 4.60 - 6.89: 63 6.89 - 9.19: 14 9.19 - 11.49: 8 Bond angle restraints: 47651 Sorted by residual: angle pdb=" N ILE F 592 " pdb=" CA ILE F 592 " pdb=" C ILE F 592 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA THR B 24 " pdb=" C THR B 24 " pdb=" O THR B 24 " ideal model delta sigma weight residual 122.36 117.61 4.75 1.21e+00 6.83e-01 1.54e+01 angle pdb=" PA ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA ARG C 235 " pdb=" C ARG C 235 " pdb=" O ARG C 235 " ideal model delta sigma weight residual 120.42 117.03 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.49 9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 47646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 21521 34.25 - 68.50: 242 68.50 - 102.75: 14 102.75 - 137.00: 9 137.00 - 171.26: 2 Dihedral angle restraints: 21788 sinusoidal: 9108 harmonic: 12680 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 111.26 -171.26 1 2.00e+01 2.50e-03 4.77e+01 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 -120.81 -147.64 1 2.00e+01 2.50e-03 4.43e+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 -132.68 -135.77 1 2.00e+01 2.50e-03 4.12e+01 ... (remaining 21785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4829 0.070 - 0.139: 509 0.139 - 0.209: 10 0.209 - 0.278: 7 0.278 - 0.348: 9 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2' ATP E 901 " pdb=" C1' ATP E 901 " pdb=" C3' ATP E 901 " pdb=" O2' ATP E 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5361 not shown) Planarity restraints: 6206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 506 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.022 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 1.46e-02 2.13e+00 pdb=" C LEU C 234 " 0.025 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=" C GLY B 554 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 555 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.020 5.00e-02 4.00e+02 ... (remaining 6203 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 372 2.55 - 3.13: 29897 3.13 - 3.72: 53278 3.72 - 4.31: 70418 4.31 - 4.90: 120627 Nonbonded interactions: 274592 Sorted by model distance: nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.958 3.040 nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.963 3.040 nonbonded pdb=" OG1 THR B 262 " pdb=" O3G ATP B 901 " model vdw 1.977 3.040 nonbonded pdb=" OG SER G 351 " pdb=" OE2 GLU G 354 " model vdw 1.982 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 1.995 3.040 ... (remaining 274587 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 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) selection = (chain 'L' and resid 301 through 373) } 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.190 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.003 0.111 35229 Z= 0.155 Angle : 0.527 11.489 47657 Z= 0.250 Chirality : 0.043 0.348 5364 Planarity : 0.003 0.040 6206 Dihedral : 11.089 171.256 13578 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 1.34 % Allowed : 4.62 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.81 (0.14), residues: 4330 helix: 2.38 (0.12), residues: 2065 sheet: -0.13 (0.21), residues: 615 loop : 0.32 (0.17), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 272 TYR 0.010 0.001 TYR B 254 PHE 0.009 0.001 PHE G 527 TRP 0.007 0.001 TRP E 561 HIS 0.002 0.001 HIS G 528 Details of bonding type rmsd covalent geometry : bond 0.00286 (35219) covalent geometry : angle 0.52663 (47651) hydrogen bonds : bond 0.14842 ( 1622) hydrogen bonds : angle 5.62006 ( 4602) metal coordination : bond 0.06280 ( 8) metal coordination : angle 2.52194 ( 6) Misc. bond : bond 0.08651 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 492 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TYR cc_start: 0.6902 (m-80) cc_final: 0.6682 (m-10) REVERT: A 161 HIS cc_start: 0.6251 (m90) cc_final: 0.5967 (m-70) REVERT: A 173 PHE cc_start: 0.7196 (m-80) cc_final: 0.6187 (m-80) REVERT: A 223 MET cc_start: 0.8727 (mmm) cc_final: 0.8389 (mmm) REVERT: A 283 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 302 GLU cc_start: 0.8854 (tt0) cc_final: 0.8651 (mt-10) REVERT: B 283 GLU cc_start: 0.7317 (tt0) cc_final: 0.7109 (tt0) REVERT: B 504 GLU cc_start: 0.8652 (tt0) cc_final: 0.8266 (mm-30) REVERT: B 571 ASP cc_start: 0.8347 (t0) cc_final: 0.8072 (t0) REVERT: C 345 MET cc_start: 0.8054 (ptp) cc_final: 0.7749 (ptt) REVERT: C 571 ASP cc_start: 0.8588 (t0) cc_final: 0.8377 (t0) REVERT: D 301 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 493 ASP cc_start: 0.8207 (m-30) cc_final: 0.7606 (t70) REVERT: D 522 LYS cc_start: 0.8471 (tttt) cc_final: 0.8214 (tptm) REVERT: D 628 PHE cc_start: 0.8315 (m-80) cc_final: 0.7968 (m-10) REVERT: E 315 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 346 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7750 (ptmt) REVERT: E 440 ILE cc_start: 0.7487 (mt) cc_final: 0.7285 (tt) REVERT: F 253 MET cc_start: 0.8321 (mtp) cc_final: 0.7871 (mtp) REVERT: F 323 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.6790 (tpt90) REVERT: F 346 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (mmtt) REVERT: F 437 MET cc_start: 0.7998 (tmm) cc_final: 0.7599 (tpp) REVERT: F 560 MET cc_start: 0.8073 (mtt) cc_final: 0.7848 (mtt) REVERT: G 138 LYS cc_start: 0.9156 (ptmm) cc_final: 0.8934 (pttm) REVERT: G 142 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8466 (pmm-80) REVERT: G 257 MET cc_start: 0.8445 (mmp) cc_final: 0.7569 (mmp) REVERT: G 378 SER cc_start: 0.7703 (m) cc_final: 0.7310 (t) REVERT: G 406 GLU cc_start: 0.8338 (tt0) cc_final: 0.8060 (tt0) outliers start: 50 outliers final: 11 residues processed: 529 average time/residue: 0.2265 time to fit residues: 186.9557 Evaluate side-chains 312 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 298 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN C 432 GLN E 295 ASN E 327 ASN E 337 GLN G 361 HIS K 240 GLN K 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079565 restraints weight = 107092.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078989 restraints weight = 61122.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079886 restraints weight = 58863.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079964 restraints weight = 44004.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081125 restraints weight = 40166.664| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 35229 Z= 0.239 Angle : 0.676 8.274 47657 Z= 0.337 Chirality : 0.046 0.170 5364 Planarity : 0.005 0.056 6206 Dihedral : 10.031 174.161 5024 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 1.83 % Allowed : 7.44 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.30 (0.13), residues: 4330 helix: 1.84 (0.12), residues: 2106 sheet: -0.16 (0.21), residues: 604 loop : 0.09 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 241 TYR 0.021 0.002 TYR G 439 PHE 0.021 0.002 PHE G 169 TRP 0.013 0.002 TRP B 486 HIS 0.014 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00559 (35219) covalent geometry : angle 0.67495 (47651) hydrogen bonds : bond 0.04336 ( 1622) hydrogen bonds : angle 4.95703 ( 4602) metal coordination : bond 0.04312 ( 8) metal coordination : angle 3.06578 ( 6) Misc. bond : bond 0.00764 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 1.081 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 158 LYS cc_start: 0.7893 (tptp) cc_final: 0.7404 (tptt) REVERT: A 173 PHE cc_start: 0.7014 (m-80) cc_final: 0.6323 (m-80) REVERT: A 283 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 430 MET cc_start: 0.9063 (tpp) cc_final: 0.8442 (tpp) REVERT: A 440 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7399 (mp) REVERT: B 571 ASP cc_start: 0.8454 (t0) cc_final: 0.8093 (t0) REVERT: B 621 MET cc_start: 0.8652 (tpp) cc_final: 0.7915 (tpp) REVERT: C 56 MET cc_start: 0.6238 (ptt) cc_final: 0.5725 (tmm) REVERT: C 342 MET cc_start: 0.9171 (mmp) cc_final: 0.8970 (mmt) REVERT: C 494 GLU cc_start: 0.8017 (pm20) cc_final: 0.7166 (pt0) REVERT: C 571 ASP cc_start: 0.8641 (t0) cc_final: 0.8282 (t0) REVERT: D 208 MET cc_start: 0.6319 (tpp) cc_final: 0.5024 (tpt) REVERT: D 304 GLU cc_start: 0.8158 (tp30) cc_final: 0.7898 (tp30) REVERT: D 493 ASP cc_start: 0.7955 (m-30) cc_final: 0.7595 (t70) REVERT: D 522 LYS cc_start: 0.8525 (tttt) cc_final: 0.8176 (tptm) REVERT: D 618 MET cc_start: 0.9045 (ttm) cc_final: 0.8826 (ttm) REVERT: E 346 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7483 (ptmm) REVERT: F 323 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7190 (tpt90) REVERT: F 588 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: G 142 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8421 (ptt-90) REVERT: G 233 MET cc_start: 0.8951 (mmm) cc_final: 0.8680 (mmm) REVERT: G 257 MET cc_start: 0.8262 (mmp) cc_final: 0.7815 (mmp) REVERT: G 378 SER cc_start: 0.7770 (m) cc_final: 0.7406 (t) REVERT: G 401 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9263 (t) REVERT: G 406 GLU cc_start: 0.8293 (tt0) cc_final: 0.7963 (tm-30) REVERT: G 422 MET cc_start: 0.8926 (mmt) cc_final: 0.8605 (mmt) REVERT: G 440 MET cc_start: 0.8152 (ttm) cc_final: 0.7689 (mtp) REVERT: H 252 ARG cc_start: 0.6226 (mmt-90) cc_final: 0.5022 (mtm180) outliers start: 68 outliers final: 33 residues processed: 359 average time/residue: 0.2058 time to fit residues: 120.4374 Evaluate side-chains 306 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 381 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN G 491 ASN K 240 GLN L 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.101609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078902 restraints weight = 105680.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080217 restraints weight = 56828.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080277 restraints weight = 50459.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080652 restraints weight = 39105.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.081544 restraints weight = 35210.859| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35229 Z= 0.159 Angle : 0.599 9.661 47657 Z= 0.293 Chirality : 0.043 0.185 5364 Planarity : 0.004 0.060 6206 Dihedral : 9.461 163.803 5005 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 1.80 % Allowed : 8.65 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.22 (0.13), residues: 4330 helix: 1.73 (0.12), residues: 2114 sheet: -0.13 (0.21), residues: 606 loop : 0.06 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 241 TYR 0.017 0.001 TYR G 439 PHE 0.013 0.001 PHE D 628 TRP 0.011 0.001 TRP B 486 HIS 0.013 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00366 (35219) covalent geometry : angle 0.59793 (47651) hydrogen bonds : bond 0.03730 ( 1622) hydrogen bonds : angle 4.65656 ( 4602) metal coordination : bond 0.03054 ( 8) metal coordination : angle 3.04973 ( 6) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 1.493 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 158 LYS cc_start: 0.7949 (tptp) cc_final: 0.7521 (tptt) REVERT: A 173 PHE cc_start: 0.6822 (m-80) cc_final: 0.6574 (m-80) REVERT: A 283 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 430 MET cc_start: 0.8986 (tpp) cc_final: 0.8450 (tpp) REVERT: A 437 MET cc_start: 0.7622 (tmm) cc_final: 0.7240 (tpt) REVERT: A 673 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7841 (ptpp) REVERT: A 784 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6857 (mpp) REVERT: B 571 ASP cc_start: 0.8432 (t0) cc_final: 0.8024 (t0) REVERT: B 621 MET cc_start: 0.8699 (tpp) cc_final: 0.8451 (tpp) REVERT: C 56 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5743 (tmm) REVERT: C 215 ASP cc_start: 0.8572 (t0) cc_final: 0.8349 (t0) REVERT: C 571 ASP cc_start: 0.8682 (t0) cc_final: 0.8327 (t0) REVERT: D 285 MET cc_start: 0.8888 (mmm) cc_final: 0.8321 (tpp) REVERT: D 493 ASP cc_start: 0.7952 (m-30) cc_final: 0.7577 (t70) REVERT: D 522 LYS cc_start: 0.8602 (tttt) cc_final: 0.8146 (tptm) REVERT: D 615 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9141 (mm) REVERT: D 618 MET cc_start: 0.9114 (ttm) cc_final: 0.8892 (ttm) REVERT: E 332 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: E 346 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7371 (ptmm) REVERT: E 489 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7916 (p) REVERT: F 323 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7275 (tpt170) REVERT: F 430 MET cc_start: 0.8946 (tpp) cc_final: 0.8684 (tpp) REVERT: F 588 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: G 233 MET cc_start: 0.8856 (mmm) cc_final: 0.8554 (mmm) REVERT: G 257 MET cc_start: 0.8327 (mmp) cc_final: 0.7796 (mmp) REVERT: G 378 SER cc_start: 0.7843 (m) cc_final: 0.7461 (t) REVERT: G 406 GLU cc_start: 0.8329 (tt0) cc_final: 0.8033 (tm-30) REVERT: G 422 MET cc_start: 0.8946 (mmt) cc_final: 0.8558 (mmt) REVERT: H 252 ARG cc_start: 0.6278 (mmt-90) cc_final: 0.4951 (mtm180) REVERT: L 352 ASP cc_start: 0.6892 (m-30) cc_final: 0.6640 (t0) outliers start: 67 outliers final: 36 residues processed: 331 average time/residue: 0.2077 time to fit residues: 114.1039 Evaluate side-chains 300 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 0.0070 chunk 144 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN G 362 GLN K 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076288 restraints weight = 105139.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078308 restraints weight = 55396.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079572 restraints weight = 37506.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080373 restraints weight = 29699.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080774 restraints weight = 25778.420| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35229 Z= 0.120 Angle : 0.565 9.316 47657 Z= 0.273 Chirality : 0.042 0.207 5364 Planarity : 0.004 0.061 6206 Dihedral : 8.999 154.193 4999 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 1.69 % Allowed : 9.83 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.30 (0.13), residues: 4330 helix: 1.81 (0.12), residues: 2099 sheet: -0.06 (0.21), residues: 613 loop : 0.08 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 142 TYR 0.016 0.001 TYR G 439 PHE 0.012 0.001 PHE H 300 TRP 0.010 0.001 TRP D 486 HIS 0.006 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00273 (35219) covalent geometry : angle 0.56415 (47651) hydrogen bonds : bond 0.03219 ( 1622) hydrogen bonds : angle 4.40512 ( 4602) metal coordination : bond 0.02259 ( 8) metal coordination : angle 2.88022 ( 6) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 1.296 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 158 LYS cc_start: 0.8498 (tptp) cc_final: 0.8012 (mmtt) REVERT: A 162 PHE cc_start: 0.2363 (p90) cc_final: 0.2112 (p90) REVERT: A 173 PHE cc_start: 0.7171 (m-80) cc_final: 0.6789 (m-80) REVERT: A 223 MET cc_start: 0.8784 (mmm) cc_final: 0.8216 (mmm) REVERT: A 283 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 673 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7857 (ptpp) REVERT: B 301 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 571 ASP cc_start: 0.8385 (t0) cc_final: 0.7966 (t0) REVERT: B 621 MET cc_start: 0.8709 (tpp) cc_final: 0.8401 (tpp) REVERT: B 762 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7563 (tmm) REVERT: C 215 ASP cc_start: 0.8694 (t0) cc_final: 0.8306 (t0) REVERT: C 571 ASP cc_start: 0.8562 (t0) cc_final: 0.8159 (t0) REVERT: C 784 MET cc_start: 0.8368 (tmm) cc_final: 0.8057 (mmt) REVERT: D 208 MET cc_start: 0.6011 (tpp) cc_final: 0.4717 (tpt) REVERT: D 304 GLU cc_start: 0.8055 (tp30) cc_final: 0.7818 (tp30) REVERT: D 345 MET cc_start: 0.8183 (tmm) cc_final: 0.7822 (tmm) REVERT: D 493 ASP cc_start: 0.8061 (m-30) cc_final: 0.7681 (t70) REVERT: D 522 LYS cc_start: 0.8645 (tttt) cc_final: 0.8037 (tptm) REVERT: D 618 MET cc_start: 0.9138 (ttm) cc_final: 0.8917 (ttm) REVERT: D 621 MET cc_start: 0.7481 (tpt) cc_final: 0.7181 (tpt) REVERT: E 332 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8157 (ttm-80) REVERT: E 489 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7879 (p) REVERT: F 323 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.7227 (tpt170) REVERT: F 430 MET cc_start: 0.8900 (tpp) cc_final: 0.8656 (tpp) REVERT: F 588 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: G 257 MET cc_start: 0.8236 (mmp) cc_final: 0.7783 (mmp) REVERT: G 352 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8048 (p) REVERT: G 378 SER cc_start: 0.8058 (m) cc_final: 0.7760 (t) REVERT: G 406 GLU cc_start: 0.8241 (tt0) cc_final: 0.7896 (tm-30) REVERT: G 440 MET cc_start: 0.7947 (ttm) cc_final: 0.7607 (mtp) REVERT: H 252 ARG cc_start: 0.6372 (mmt-90) cc_final: 0.4939 (mtm180) outliers start: 63 outliers final: 36 residues processed: 334 average time/residue: 0.2020 time to fit residues: 112.4093 Evaluate side-chains 305 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 411 optimal weight: 0.3980 chunk 67 optimal weight: 0.0270 chunk 271 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 432 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS G 289 GLN G 344 HIS G 362 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.102905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077103 restraints weight = 104701.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079119 restraints weight = 54416.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080313 restraints weight = 36505.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081156 restraints weight = 29048.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081578 restraints weight = 25151.911| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35229 Z= 0.103 Angle : 0.555 9.798 47657 Z= 0.266 Chirality : 0.042 0.222 5364 Planarity : 0.004 0.080 6206 Dihedral : 8.636 144.891 4995 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 1.66 % Allowed : 10.71 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.34 (0.13), residues: 4330 helix: 1.82 (0.12), residues: 2092 sheet: 0.01 (0.21), residues: 626 loop : 0.12 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 348 TYR 0.013 0.001 TYR G 439 PHE 0.013 0.001 PHE G 509 TRP 0.010 0.001 TRP D 486 HIS 0.008 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00228 (35219) covalent geometry : angle 0.55397 (47651) hydrogen bonds : bond 0.02905 ( 1622) hydrogen bonds : angle 4.24860 ( 4602) metal coordination : bond 0.01454 ( 8) metal coordination : angle 3.28627 ( 6) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8650 (tptp) cc_final: 0.8299 (tptt) REVERT: A 173 PHE cc_start: 0.7291 (m-80) cc_final: 0.6797 (m-80) REVERT: A 223 MET cc_start: 0.8759 (mmm) cc_final: 0.8141 (mmm) REVERT: A 283 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 673 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7793 (ptpp) REVERT: B 301 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 571 ASP cc_start: 0.8312 (t0) cc_final: 0.7830 (t0) REVERT: B 621 MET cc_start: 0.8629 (tpp) cc_final: 0.8289 (tpp) REVERT: B 762 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7570 (tmm) REVERT: C 215 ASP cc_start: 0.8769 (t0) cc_final: 0.8435 (t0) REVERT: C 342 MET cc_start: 0.9194 (mmm) cc_final: 0.8984 (mmt) REVERT: C 398 MET cc_start: 0.9126 (mmt) cc_final: 0.8896 (mmt) REVERT: C 571 ASP cc_start: 0.8401 (t0) cc_final: 0.8072 (t0) REVERT: D 259 THR cc_start: 0.9171 (p) cc_final: 0.8965 (t) REVERT: D 304 GLU cc_start: 0.8053 (tp30) cc_final: 0.7847 (tp30) REVERT: D 345 MET cc_start: 0.8238 (tmm) cc_final: 0.7903 (tmm) REVERT: D 493 ASP cc_start: 0.8020 (m-30) cc_final: 0.7629 (t70) REVERT: D 522 LYS cc_start: 0.8631 (tttt) cc_final: 0.7977 (tptm) REVERT: D 621 MET cc_start: 0.7478 (tpt) cc_final: 0.6986 (tpt) REVERT: E 617 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: F 430 MET cc_start: 0.8891 (tpp) cc_final: 0.8648 (tpp) REVERT: G 257 MET cc_start: 0.8219 (mmp) cc_final: 0.7786 (mmp) REVERT: G 352 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7977 (p) REVERT: G 378 SER cc_start: 0.7870 (m) cc_final: 0.7515 (t) REVERT: G 406 GLU cc_start: 0.8286 (tt0) cc_final: 0.7945 (tm-30) REVERT: G 440 MET cc_start: 0.7907 (ttm) cc_final: 0.7606 (mtp) REVERT: H 252 ARG cc_start: 0.6463 (mmt-90) cc_final: 0.5025 (mtm180) REVERT: L 351 GLU cc_start: 0.7201 (pm20) cc_final: 0.6848 (tp30) outliers start: 62 outliers final: 35 residues processed: 345 average time/residue: 0.1948 time to fit residues: 113.2841 Evaluate side-chains 301 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 292 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 428 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 397 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN G 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078277 restraints weight = 105376.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080113 restraints weight = 58353.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079987 restraints weight = 47587.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080265 restraints weight = 38647.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080548 restraints weight = 34303.487| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35229 Z= 0.166 Angle : 0.594 11.372 47657 Z= 0.287 Chirality : 0.043 0.277 5364 Planarity : 0.004 0.060 6206 Dihedral : 8.466 137.883 4995 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 2.07 % Allowed : 10.93 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.23 (0.13), residues: 4330 helix: 1.73 (0.12), residues: 2103 sheet: -0.01 (0.21), residues: 615 loop : 0.04 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 348 TYR 0.016 0.001 TYR G 439 PHE 0.022 0.001 PHE G 509 TRP 0.012 0.001 TRP B 486 HIS 0.005 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00383 (35219) covalent geometry : angle 0.59308 (47651) hydrogen bonds : bond 0.03310 ( 1622) hydrogen bonds : angle 4.35524 ( 4602) metal coordination : bond 0.03157 ( 8) metal coordination : angle 2.97336 ( 6) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7823 (tptp) cc_final: 0.7307 (tptt) REVERT: A 223 MET cc_start: 0.8768 (mmm) cc_final: 0.8547 (tpp) REVERT: A 283 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 673 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7842 (ptpp) REVERT: A 784 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6413 (mpp) REVERT: B 331 GLU cc_start: 0.8256 (mp0) cc_final: 0.8054 (mt-10) REVERT: B 558 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 571 ASP cc_start: 0.8442 (t0) cc_final: 0.7947 (t0) REVERT: B 621 MET cc_start: 0.8793 (tpp) cc_final: 0.8292 (tpp) REVERT: B 762 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7598 (tmm) REVERT: C 215 ASP cc_start: 0.8812 (t0) cc_final: 0.8495 (t0) REVERT: C 223 MET cc_start: 0.8935 (tpp) cc_final: 0.8690 (mmm) REVERT: C 571 ASP cc_start: 0.8554 (t0) cc_final: 0.8186 (t0) REVERT: C 784 MET cc_start: 0.8339 (tmm) cc_final: 0.8004 (mmt) REVERT: D 208 MET cc_start: 0.6155 (tpp) cc_final: 0.5035 (tpt) REVERT: D 345 MET cc_start: 0.8312 (tmm) cc_final: 0.7958 (tmm) REVERT: D 493 ASP cc_start: 0.7986 (m-30) cc_final: 0.7541 (t70) REVERT: D 522 LYS cc_start: 0.8613 (tttt) cc_final: 0.8081 (tptm) REVERT: D 621 MET cc_start: 0.7492 (tpt) cc_final: 0.6945 (tpt) REVERT: E 489 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7983 (p) REVERT: E 617 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: F 430 MET cc_start: 0.8885 (tpp) cc_final: 0.8635 (tpp) REVERT: G 257 MET cc_start: 0.8316 (mmp) cc_final: 0.7749 (mmp) REVERT: G 352 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8087 (p) REVERT: G 378 SER cc_start: 0.7947 (m) cc_final: 0.7375 (t) REVERT: G 406 GLU cc_start: 0.8426 (tt0) cc_final: 0.8186 (tt0) REVERT: H 252 ARG cc_start: 0.6610 (mmt-90) cc_final: 0.5152 (mtm110) outliers start: 77 outliers final: 54 residues processed: 324 average time/residue: 0.1879 time to fit residues: 104.1632 Evaluate side-chains 320 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 31 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 252 optimal weight: 1.9990 chunk 290 optimal weight: 0.4980 chunk 366 optimal weight: 0.7980 chunk 378 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN G 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075345 restraints weight = 106564.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077308 restraints weight = 56197.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078597 restraints weight = 38065.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079283 restraints weight = 30036.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079802 restraints weight = 26397.146| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35229 Z= 0.142 Angle : 0.583 10.892 47657 Z= 0.280 Chirality : 0.043 0.239 5364 Planarity : 0.004 0.060 6206 Dihedral : 8.324 136.147 4995 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 1.93 % Allowed : 11.25 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.20 (0.13), residues: 4330 helix: 1.70 (0.12), residues: 2099 sheet: 0.01 (0.21), residues: 619 loop : 0.03 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 142 TYR 0.015 0.001 TYR G 439 PHE 0.020 0.001 PHE G 509 TRP 0.010 0.001 TRP B 486 HIS 0.004 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00326 (35219) covalent geometry : angle 0.58184 (47651) hydrogen bonds : bond 0.03165 ( 1622) hydrogen bonds : angle 4.31647 ( 4602) metal coordination : bond 0.02756 ( 8) metal coordination : angle 3.15820 ( 6) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8422 (tptp) cc_final: 0.8060 (tptt) REVERT: A 283 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 673 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7862 (ptpp) REVERT: A 784 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6336 (mpp) REVERT: B 301 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 571 ASP cc_start: 0.8374 (t0) cc_final: 0.7880 (t0) REVERT: B 621 MET cc_start: 0.8813 (tpp) cc_final: 0.8366 (tpp) REVERT: B 762 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7484 (tmm) REVERT: C 215 ASP cc_start: 0.8901 (t0) cc_final: 0.8596 (t0) REVERT: C 398 MET cc_start: 0.9119 (mmt) cc_final: 0.8867 (mmt) REVERT: C 571 ASP cc_start: 0.8495 (t0) cc_final: 0.8125 (t0) REVERT: D 345 MET cc_start: 0.8266 (tmm) cc_final: 0.7944 (tmm) REVERT: D 493 ASP cc_start: 0.7900 (m-30) cc_final: 0.7530 (t70) REVERT: D 522 LYS cc_start: 0.8632 (tttt) cc_final: 0.8022 (tptm) REVERT: D 621 MET cc_start: 0.7450 (tpt) cc_final: 0.6962 (tpt) REVERT: E 489 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7885 (p) REVERT: E 617 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: F 430 MET cc_start: 0.8900 (tpp) cc_final: 0.8633 (tpp) REVERT: G 257 MET cc_start: 0.8227 (mmp) cc_final: 0.7786 (mmp) REVERT: G 352 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8075 (p) REVERT: G 378 SER cc_start: 0.8109 (m) cc_final: 0.7693 (t) REVERT: G 406 GLU cc_start: 0.8257 (tt0) cc_final: 0.7979 (tt0) REVERT: G 440 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: H 238 MET cc_start: 0.8598 (ttm) cc_final: 0.8271 (tpp) REVERT: H 252 ARG cc_start: 0.6729 (mmt-90) cc_final: 0.5048 (mtm110) outliers start: 72 outliers final: 55 residues processed: 319 average time/residue: 0.1863 time to fit residues: 101.7066 Evaluate side-chains 320 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 440 MET Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 344 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 422 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 423 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** 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 = 0.3693 r_free = 0.3693 target = 0.101033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075220 restraints weight = 105558.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077166 restraints weight = 55463.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078430 restraints weight = 37518.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079233 restraints weight = 29515.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079652 restraints weight = 25680.653| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35229 Z= 0.155 Angle : 0.599 10.871 47657 Z= 0.287 Chirality : 0.043 0.222 5364 Planarity : 0.004 0.060 6206 Dihedral : 8.242 135.499 4995 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.01 % Allowed : 11.39 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.17 (0.13), residues: 4330 helix: 1.70 (0.12), residues: 2093 sheet: -0.05 (0.21), residues: 618 loop : 0.01 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 648 TYR 0.015 0.001 TYR G 439 PHE 0.018 0.001 PHE G 509 TRP 0.012 0.001 TRP B 486 HIS 0.004 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00357 (35219) covalent geometry : angle 0.59757 (47651) hydrogen bonds : bond 0.03243 ( 1622) hydrogen bonds : angle 4.33930 ( 4602) metal coordination : bond 0.02979 ( 8) metal coordination : angle 3.42053 ( 6) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 259 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8528 (tptp) cc_final: 0.8186 (tptt) REVERT: A 283 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 673 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7858 (ptpp) REVERT: A 784 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6356 (mpp) REVERT: B 301 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 571 ASP cc_start: 0.8386 (t0) cc_final: 0.7897 (t0) REVERT: B 621 MET cc_start: 0.8837 (tpp) cc_final: 0.8395 (tpp) REVERT: B 762 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7599 (tmm) REVERT: C 215 ASP cc_start: 0.8919 (t0) cc_final: 0.8625 (t0) REVERT: C 398 MET cc_start: 0.9127 (mmt) cc_final: 0.8871 (mmt) REVERT: C 571 ASP cc_start: 0.8513 (t0) cc_final: 0.8137 (t0) REVERT: C 784 MET cc_start: 0.8391 (tmm) cc_final: 0.8020 (mmt) REVERT: D 208 MET cc_start: 0.6165 (tpp) cc_final: 0.4540 (tpt) REVERT: D 304 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: D 345 MET cc_start: 0.8249 (tmm) cc_final: 0.7834 (tmm) REVERT: D 493 ASP cc_start: 0.7928 (m-30) cc_final: 0.7536 (t70) REVERT: D 522 LYS cc_start: 0.8587 (tttt) cc_final: 0.7968 (tptm) REVERT: D 621 MET cc_start: 0.7440 (tpt) cc_final: 0.6893 (tpt) REVERT: E 489 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7905 (p) REVERT: E 514 THR cc_start: 0.8767 (m) cc_final: 0.8531 (p) REVERT: E 617 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: F 430 MET cc_start: 0.8906 (tpp) cc_final: 0.8633 (tpp) REVERT: G 257 MET cc_start: 0.8227 (mmp) cc_final: 0.7861 (mmp) REVERT: G 352 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8071 (p) REVERT: G 378 SER cc_start: 0.8217 (m) cc_final: 0.7919 (t) REVERT: G 406 GLU cc_start: 0.8226 (tt0) cc_final: 0.7953 (tt0) REVERT: G 440 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7655 (mtp) REVERT: H 238 MET cc_start: 0.8591 (ttm) cc_final: 0.8273 (tpp) REVERT: H 252 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.4981 (mtm110) REVERT: L 348 LYS cc_start: 0.6278 (mmmt) cc_final: 0.5815 (mttp) outliers start: 75 outliers final: 60 residues processed: 312 average time/residue: 0.1947 time to fit residues: 103.3442 Evaluate side-chains 322 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 440 MET Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 344 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 243 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.100923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078227 restraints weight = 105423.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079575 restraints weight = 57884.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079853 restraints weight = 48046.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080013 restraints weight = 39521.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080634 restraints weight = 35709.904| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35229 Z= 0.175 Angle : 0.616 11.799 47657 Z= 0.297 Chirality : 0.043 0.218 5364 Planarity : 0.004 0.064 6206 Dihedral : 8.237 134.789 4995 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.45 % Favored : 94.53 % Rotamer: Outliers : 1.83 % Allowed : 11.82 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.09 (0.13), residues: 4330 helix: 1.64 (0.12), residues: 2104 sheet: -0.08 (0.21), residues: 604 loop : -0.05 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 266 TYR 0.016 0.001 TYR G 439 PHE 0.019 0.001 PHE G 509 TRP 0.013 0.001 TRP B 486 HIS 0.004 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00403 (35219) covalent geometry : angle 0.61468 (47651) hydrogen bonds : bond 0.03412 ( 1622) hydrogen bonds : angle 4.41856 ( 4602) metal coordination : bond 0.03292 ( 8) metal coordination : angle 3.93008 ( 6) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7806 (tptp) cc_final: 0.7369 (tptt) REVERT: A 283 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 673 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7886 (ptpp) REVERT: A 784 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6334 (mpp) REVERT: B 571 ASP cc_start: 0.8421 (t0) cc_final: 0.7933 (t0) REVERT: B 621 MET cc_start: 0.8900 (tpp) cc_final: 0.8458 (tpp) REVERT: B 762 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7598 (tmm) REVERT: C 215 ASP cc_start: 0.8840 (t0) cc_final: 0.8596 (t0) REVERT: C 398 MET cc_start: 0.9086 (mmt) cc_final: 0.8830 (mmt) REVERT: C 571 ASP cc_start: 0.8579 (t0) cc_final: 0.8202 (t0) REVERT: C 784 MET cc_start: 0.8372 (tmm) cc_final: 0.7992 (mmt) REVERT: D 208 MET cc_start: 0.6505 (tpp) cc_final: 0.5088 (tpt) REVERT: D 345 MET cc_start: 0.8288 (tmm) cc_final: 0.7941 (tmm) REVERT: D 493 ASP cc_start: 0.7963 (m-30) cc_final: 0.7549 (t70) REVERT: D 522 LYS cc_start: 0.8586 (tttt) cc_final: 0.7964 (tptm) REVERT: E 489 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7961 (p) REVERT: E 514 THR cc_start: 0.8864 (m) cc_final: 0.8607 (p) REVERT: E 617 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: F 430 MET cc_start: 0.8896 (tpp) cc_final: 0.8634 (tpp) REVERT: G 233 MET cc_start: 0.9067 (mmm) cc_final: 0.8758 (mmm) REVERT: G 257 MET cc_start: 0.8300 (mmp) cc_final: 0.7825 (mmp) REVERT: G 352 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8126 (p) REVERT: G 378 SER cc_start: 0.7930 (m) cc_final: 0.7574 (t) REVERT: G 406 GLU cc_start: 0.8306 (tt0) cc_final: 0.8037 (tt0) REVERT: G 440 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: H 238 MET cc_start: 0.8602 (ttm) cc_final: 0.8277 (tpp) REVERT: H 252 ARG cc_start: 0.6914 (mmt-90) cc_final: 0.5027 (mtm110) REVERT: L 348 LYS cc_start: 0.6677 (mmmt) cc_final: 0.6079 (ptpt) outliers start: 68 outliers final: 58 residues processed: 309 average time/residue: 0.1931 time to fit residues: 101.5420 Evaluate side-chains 313 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 440 MET Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 374 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076136 restraints weight = 106245.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077579 restraints weight = 58145.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077661 restraints weight = 49878.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077821 restraints weight = 40361.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078532 restraints weight = 36162.491| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 35229 Z= 0.277 Angle : 0.714 12.329 47657 Z= 0.349 Chirality : 0.046 0.202 5364 Planarity : 0.004 0.064 6206 Dihedral : 8.442 134.956 4995 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 1.64 % Allowed : 12.35 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4330 helix: 1.38 (0.12), residues: 2104 sheet: -0.28 (0.21), residues: 593 loop : -0.23 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 259 TYR 0.021 0.002 TYR G 439 PHE 0.021 0.002 PHE D 275 TRP 0.023 0.002 TRP B 486 HIS 0.006 0.001 HIS F 414 Details of bonding type rmsd covalent geometry : bond 0.00639 (35219) covalent geometry : angle 0.71189 (47651) hydrogen bonds : bond 0.04102 ( 1622) hydrogen bonds : angle 4.74634 ( 4602) metal coordination : bond 0.04702 ( 8) metal coordination : angle 5.18144 ( 6) Misc. bond : bond 0.00107 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7732 (tptp) cc_final: 0.7246 (tptt) REVERT: A 283 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 784 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6448 (mpp) REVERT: B 223 MET cc_start: 0.9203 (tpp) cc_final: 0.8854 (tpt) REVERT: B 359 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8177 (ttm110) REVERT: B 571 ASP cc_start: 0.8559 (t0) cc_final: 0.8056 (t0) REVERT: B 621 MET cc_start: 0.9004 (tpp) cc_final: 0.8609 (tpp) REVERT: B 762 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: C 215 ASP cc_start: 0.8860 (t0) cc_final: 0.8626 (t0) REVERT: C 571 ASP cc_start: 0.8681 (t0) cc_final: 0.8270 (t0) REVERT: D 208 MET cc_start: 0.6538 (tpp) cc_final: 0.5269 (tpt) REVERT: D 345 MET cc_start: 0.8330 (tmm) cc_final: 0.7972 (tmm) REVERT: D 493 ASP cc_start: 0.7980 (m-30) cc_final: 0.7536 (t70) REVERT: D 522 LYS cc_start: 0.8612 (tttt) cc_final: 0.7883 (tptp) REVERT: E 489 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 514 THR cc_start: 0.8945 (m) cc_final: 0.8680 (p) REVERT: E 617 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: F 286 SER cc_start: 0.9301 (p) cc_final: 0.8950 (m) REVERT: F 430 MET cc_start: 0.8944 (tpp) cc_final: 0.8648 (tpp) REVERT: G 233 MET cc_start: 0.9065 (mmm) cc_final: 0.8838 (mmm) REVERT: G 257 MET cc_start: 0.8353 (mmp) cc_final: 0.7809 (mmp) REVERT: G 352 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8346 (p) REVERT: G 378 SER cc_start: 0.8327 (m) cc_final: 0.7942 (t) REVERT: G 406 GLU cc_start: 0.8265 (tt0) cc_final: 0.8002 (tt0) REVERT: H 238 MET cc_start: 0.8547 (ttm) cc_final: 0.8250 (tpp) REVERT: H 252 ARG cc_start: 0.6963 (mmt-90) cc_final: 0.5103 (mtm110) REVERT: L 348 LYS cc_start: 0.6815 (mmmt) cc_final: 0.5998 (ptpt) outliers start: 61 outliers final: 55 residues processed: 295 average time/residue: 0.1910 time to fit residues: 96.9303 Evaluate side-chains 305 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 440 MET Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 426 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 432 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN L 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.101099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078461 restraints weight = 105036.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079888 restraints weight = 57154.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080129 restraints weight = 47505.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080290 restraints weight = 38789.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080973 restraints weight = 35059.210| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35229 Z= 0.139 Angle : 0.618 12.727 47657 Z= 0.297 Chirality : 0.043 0.223 5364 Planarity : 0.004 0.064 6206 Dihedral : 8.272 133.175 4995 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 1.75 % Allowed : 12.35 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 4330 helix: 1.51 (0.12), residues: 2098 sheet: -0.13 (0.21), residues: 603 loop : -0.14 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 648 TYR 0.015 0.001 TYR G 439 PHE 0.022 0.001 PHE G 509 TRP 0.013 0.001 TRP D 486 HIS 0.003 0.001 HIS G 344 Details of bonding type rmsd covalent geometry : bond 0.00321 (35219) covalent geometry : angle 0.61512 (47651) hydrogen bonds : bond 0.03272 ( 1622) hydrogen bonds : angle 4.44038 ( 4602) metal coordination : bond 0.02411 ( 8) metal coordination : angle 4.86367 ( 6) Misc. bond : bond 0.00035 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.30 seconds wall clock time: 96 minutes 54.64 seconds (5814.64 seconds total)