Starting phenix.real_space_refine on Mon Jul 6 11:10:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dat_27275/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_2026/8dat_27275.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dat_27275/07_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-6108/lib/python3.11/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: 7.79, 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 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: 1.12 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: 8.09 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 21435 34.25 - 68.50: 178 68.50 - 102.75: 9 102.75 - 137.00: 9 137.00 - 171.26: 2 Dihedral angle restraints: 21633 sinusoidal: 8953 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 21630 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: 6.170 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: 0.050 Extract box with map and model: 0.760 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.000 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 10.339 171.256 13423 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/Z covalent geometry : bond 0.00286 / 0.14 (35219) covalent geometry : angle 0.52663 / 0.25 (47651) hydrogen bonds : bond 0.14842 / 9.97 ( 1622) hydrogen bonds : angle 5.62006 / 3.94 ( 4602) metal coordination : bond 0.06280 / 3.10 ( 8) metal coordination : angle 2.52194 / 1.42 ( 6) Misc. bond : bond 0.08651 / 4.39 ( 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 : 1.514 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: 0.2492 time to fit residues: 205.1847 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 : 1.387 ------------------------------------------------------------------------------- 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... A 337 GLN C 432 GLN E 295 ASN E 327 ASN E 337 GLN G 361 HIS K 240 GLN K 241 GLN L 325 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078876 restraints weight = 106949.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079731 restraints weight = 59347.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079678 restraints weight = 60000.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080174 restraints weight = 44863.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081071 restraints weight = 39423.754| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 35229 Z= 0.236 Angle : 0.675 8.615 47657 Z= 0.336 Chirality : 0.046 0.168 5364 Planarity : 0.005 0.056 6206 Dihedral : 8.634 173.728 4869 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 1.96 % Allowed : 7.30 % 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: 1.26 (0.13), residues: 4330 helix: 1.79 (0.12), residues: 2106 sheet: -0.23 (0.21), residues: 613 loop : 0.11 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 348 TYR 0.023 0.002 TYR G 439 PHE 0.022 0.002 PHE G 169 TRP 0.013 0.002 TRP B 486 HIS 0.011 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 (35219) covalent geometry : angle 0.67378 / 0.34 (47651) hydrogen bonds : bond 0.04360 / 2.92 ( 1622) hydrogen bonds : angle 4.94685 / 3.46 ( 4602) metal coordination : bond 0.04391 / 1.94 ( 8) metal coordination : angle 3.16723 / 2.96 ( 6) Misc. bond : bond 0.01342 / 0.67 ( 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 381 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7815 (tptp) cc_final: 0.7323 (tptt) REVERT: A 173 PHE cc_start: 0.7071 (m-80) cc_final: 0.6304 (m-80) REVERT: A 283 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 430 MET cc_start: 0.9065 (tpp) cc_final: 0.8457 (tpp) REVERT: A 440 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7394 (mp) REVERT: B 571 ASP cc_start: 0.8491 (t0) cc_final: 0.8127 (t0) REVERT: B 621 MET cc_start: 0.8713 (tpp) cc_final: 0.8306 (tpp) REVERT: C 56 MET cc_start: 0.6227 (ptt) cc_final: 0.5715 (tmm) REVERT: C 342 MET cc_start: 0.9188 (mmp) cc_final: 0.8979 (mmt) REVERT: C 494 GLU cc_start: 0.7992 (pm20) cc_final: 0.7167 (pt0) REVERT: C 571 ASP cc_start: 0.8686 (t0) cc_final: 0.8326 (t0) REVERT: D 208 MET cc_start: 0.6282 (tpp) cc_final: 0.4967 (tpt) REVERT: D 304 GLU cc_start: 0.8139 (tp30) cc_final: 0.7871 (tp30) REVERT: D 493 ASP cc_start: 0.7947 (m-30) cc_final: 0.7603 (t70) REVERT: D 522 LYS cc_start: 0.8551 (tttt) cc_final: 0.8199 (tptm) REVERT: D 618 MET cc_start: 0.9076 (ttm) cc_final: 0.8872 (ttm) REVERT: E 346 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (ptmm) REVERT: E 608 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6450 (p0) REVERT: F 323 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.7157 (tpt90) REVERT: F 588 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: G 142 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8400 (ptt-90) REVERT: G 233 MET cc_start: 0.8980 (mmm) cc_final: 0.8703 (mmm) REVERT: G 257 MET cc_start: 0.8323 (mmp) cc_final: 0.7853 (mmp) REVERT: G 378 SER cc_start: 0.7921 (m) cc_final: 0.7585 (t) REVERT: G 406 GLU cc_start: 0.8264 (tt0) cc_final: 0.7921 (tm-30) REVERT: G 422 MET cc_start: 0.8987 (mmt) cc_final: 0.8718 (mmt) REVERT: G 440 MET cc_start: 0.8124 (ttm) cc_final: 0.7721 (mtp) REVERT: H 252 ARG cc_start: 0.6212 (mmt-90) cc_final: 0.4989 (mtm180) outliers start: 73 outliers final: 36 residues processed: 365 average time/residue: 0.2258 time to fit residues: 134.0647 Evaluate side-chains 307 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 302 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 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 570 GLN 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 Chi-restraints excluded: chain L residue 354 ARG 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: 0.1980 chunk 328 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 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: 3.9990 chunk 185 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 548 ASN B 651 GLN C 161 HIS C 548 ASN G 206 ASN G 491 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.102858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081202 restraints weight = 106256.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080567 restraints weight = 61041.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081332 restraints weight = 54914.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081936 restraints weight = 42420.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081992 restraints weight = 37797.280| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35229 Z= 0.125 Angle : 0.583 11.058 47657 Z= 0.282 Chirality : 0.043 0.189 5364 Planarity : 0.004 0.058 6206 Dihedral : 8.045 162.521 4853 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 1.66 % Allowed : 8.67 % Favored : 89.66 % 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: 1.31 (0.13), residues: 4330 helix: 1.83 (0.12), residues: 2102 sheet: -0.12 (0.21), residues: 614 loop : 0.11 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 348 TYR 0.014 0.001 TYR G 439 PHE 0.012 0.001 PHE D 628 TRP 0.009 0.001 TRP D 486 HIS 0.014 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (35219) covalent geometry : angle 0.58238 / 0.28 (47651) hydrogen bonds : bond 0.03492 / 2.33 ( 1622) hydrogen bonds : angle 4.54461 / 3.19 ( 4602) metal coordination : bond 0.02170 / 0.93 ( 8) metal coordination : angle 2.95560 / 2.51 ( 6) Misc. bond : bond 0.00134 / 0.07 ( 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 357 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7896 (tptp) cc_final: 0.7479 (tptt) REVERT: A 283 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 617 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 673 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7868 (ptpp) REVERT: A 784 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6857 (mpp) REVERT: B 301 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 571 ASP cc_start: 0.8410 (t0) cc_final: 0.8027 (t0) REVERT: B 621 MET cc_start: 0.8656 (tpp) cc_final: 0.8382 (tpp) REVERT: B 762 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7543 (tmm) REVERT: C 56 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5825 (tmm) REVERT: C 215 ASP cc_start: 0.8495 (t0) cc_final: 0.8196 (t0) REVERT: C 571 ASP cc_start: 0.8604 (t0) cc_final: 0.8255 (t0) REVERT: C 784 MET cc_start: 0.8428 (tmm) cc_final: 0.8075 (mmt) REVERT: D 493 ASP cc_start: 0.7931 (m-30) cc_final: 0.7567 (t70) REVERT: D 522 LYS cc_start: 0.8598 (tttt) cc_final: 0.8143 (tptm) REVERT: D 615 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9097 (mm) REVERT: D 618 MET cc_start: 0.9154 (ttm) cc_final: 0.8940 (ttm) REVERT: E 332 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8179 (ttm-80) REVERT: E 346 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7327 (ptmt) REVERT: E 489 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7969 (p) REVERT: F 323 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7164 (tpt170) REVERT: F 430 MET cc_start: 0.8903 (tpp) cc_final: 0.8671 (tpp) REVERT: F 588 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: G 233 MET cc_start: 0.8829 (mmm) cc_final: 0.8505 (mmm) REVERT: G 257 MET cc_start: 0.8200 (mmp) cc_final: 0.7833 (mmp) REVERT: G 378 SER cc_start: 0.7730 (m) cc_final: 0.7377 (t) REVERT: G 406 GLU cc_start: 0.8333 (tt0) cc_final: 0.8055 (tm-30) REVERT: G 422 MET cc_start: 0.8937 (mmt) cc_final: 0.8623 (mmt) REVERT: H 252 ARG cc_start: 0.6250 (mmt-90) cc_final: 0.4944 (mtm180) REVERT: L 352 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6446 (t0) outliers start: 62 outliers final: 28 residues processed: 339 average time/residue: 0.2211 time to fit residues: 123.2526 Evaluate side-chains 303 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 351 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 762 MET 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 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 676 LEU 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 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 302 GLU 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 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 352 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 370 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN K 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075443 restraints weight = 104934.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.077383 restraints weight = 55542.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078681 restraints weight = 37903.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079435 restraints weight = 29929.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079912 restraints weight = 26012.370| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35229 Z= 0.154 Angle : 0.579 9.639 47657 Z= 0.281 Chirality : 0.043 0.208 5364 Planarity : 0.004 0.061 6206 Dihedral : 7.711 152.371 4847 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.92 % Rotamer: Outliers : 1.93 % Allowed : 9.85 % Favored : 88.21 % 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: 1.75 (0.12), residues: 2104 sheet: -0.11 (0.21), residues: 614 loop : 0.04 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 142 TYR 0.017 0.001 TYR G 439 PHE 0.013 0.001 PHE D 275 TRP 0.011 0.001 TRP B 486 HIS 0.006 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (35219) covalent geometry : angle 0.57829 / 0.28 (47651) hydrogen bonds : bond 0.03418 / 2.28 ( 1622) hydrogen bonds : angle 4.45800 / 3.14 ( 4602) metal coordination : bond 0.03063 / 1.33 ( 8) metal coordination : angle 3.02226 / 2.74 ( 6) Misc. bond : bond 0.00045 / 0.02 ( 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: 72 poor density : 279 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8498 (tptp) cc_final: 0.8106 (tptt) REVERT: A 283 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 430 MET cc_start: 0.8993 (tpp) cc_final: 0.8426 (tpp) REVERT: A 673 LYS cc_start: 0.8071 (ttpp) cc_final: 0.7836 (ptpp) REVERT: B 571 ASP cc_start: 0.8413 (t0) cc_final: 0.7963 (t0) REVERT: B 621 MET cc_start: 0.8765 (tpp) cc_final: 0.8469 (tpp) REVERT: B 762 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: C 215 ASP cc_start: 0.8756 (t0) cc_final: 0.8399 (t0) REVERT: C 571 ASP cc_start: 0.8618 (t0) cc_final: 0.8203 (t0) REVERT: D 493 ASP cc_start: 0.7929 (m-30) cc_final: 0.7561 (t70) REVERT: D 522 LYS cc_start: 0.8666 (tttt) cc_final: 0.8069 (tptm) REVERT: D 615 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9044 (mm) REVERT: D 618 MET cc_start: 0.9153 (ttm) cc_final: 0.8942 (ttm) REVERT: D 621 MET cc_start: 0.7431 (tpt) cc_final: 0.7082 (tpt) REVERT: E 489 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7895 (p) REVERT: F 323 ARG cc_start: 0.7974 (tpp-160) cc_final: 0.7245 (tpt170) REVERT: F 430 MET cc_start: 0.8921 (tpp) cc_final: 0.8653 (tpp) REVERT: F 588 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: G 257 MET cc_start: 0.8245 (mmp) cc_final: 0.7775 (mmp) REVERT: G 352 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8120 (p) REVERT: G 378 SER cc_start: 0.8115 (m) cc_final: 0.7846 (t) REVERT: G 406 GLU cc_start: 0.8329 (tt0) cc_final: 0.7991 (tm-30) REVERT: G 440 MET cc_start: 0.8023 (ttm) cc_final: 0.7634 (mtp) REVERT: H 252 ARG cc_start: 0.6429 (mmt-90) cc_final: 0.4953 (mtm180) REVERT: L 351 GLU cc_start: 0.7419 (pm20) cc_final: 0.6963 (tp30) REVERT: L 352 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6469 (t0) outliers start: 72 outliers final: 44 residues processed: 333 average time/residue: 0.2137 time to fit residues: 118.1905 Evaluate side-chains 309 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 676 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 378 ASP 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 223 MET 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 324 ASP 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 302 GLU 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 227 GLN 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 G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 352 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 0.3980 chunk 223 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 411 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 271 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077144 restraints weight = 104710.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079153 restraints weight = 54150.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080495 restraints weight = 36412.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.081188 restraints weight = 28392.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081748 restraints weight = 24794.204| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35229 Z= 0.107 Angle : 0.557 9.524 47657 Z= 0.267 Chirality : 0.042 0.211 5364 Planarity : 0.003 0.060 6206 Dihedral : 7.435 145.220 4843 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 1.75 % Allowed : 10.63 % 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: 1.32 (0.13), residues: 4330 helix: 1.82 (0.12), residues: 2097 sheet: 0.03 (0.21), residues: 615 loop : 0.07 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 348 TYR 0.014 0.001 TYR G 439 PHE 0.011 0.001 PHE H 300 TRP 0.010 0.001 TRP D 486 HIS 0.010 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (35219) covalent geometry : angle 0.55643 / 0.27 (47651) hydrogen bonds : bond 0.02991 / 1.99 ( 1622) hydrogen bonds : angle 4.28109 / 3.02 ( 4602) metal coordination : bond 0.01818 / 0.78 ( 8) metal coordination : angle 2.74565 / 2.29 ( 6) Misc. bond : bond 0.00020 / 0.01 ( 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 352 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 1.394 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: 0.8582 (tptp) cc_final: 0.8224 (tptt) REVERT: A 283 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 673 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7802 (ptpp) REVERT: B 301 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 571 ASP cc_start: 0.8335 (t0) cc_final: 0.7846 (t0) REVERT: B 621 MET cc_start: 0.8698 (tpp) cc_final: 0.8361 (tpp) REVERT: B 762 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: C 215 ASP cc_start: 0.8832 (t0) cc_final: 0.8453 (t0) REVERT: C 342 MET cc_start: 0.9217 (mmm) cc_final: 0.8998 (mmt) REVERT: C 398 MET cc_start: 0.9128 (mmt) cc_final: 0.8858 (mmt) REVERT: C 437 MET cc_start: 0.8416 (tpp) cc_final: 0.8145 (tpp) REVERT: C 571 ASP cc_start: 0.8495 (t0) cc_final: 0.8148 (t0) REVERT: C 784 MET cc_start: 0.8327 (tmm) cc_final: 0.8047 (mmt) REVERT: D 208 MET cc_start: 0.6057 (tpp) cc_final: 0.4322 (tpt) REVERT: D 493 ASP cc_start: 0.8033 (m-30) cc_final: 0.7624 (t70) REVERT: D 522 LYS cc_start: 0.8631 (tttt) cc_final: 0.7971 (tptm) REVERT: D 618 MET cc_start: 0.9126 (ttm) cc_final: 0.8906 (ttm) REVERT: D 621 MET cc_start: 0.7448 (tpt) cc_final: 0.7090 (tpt) REVERT: E 223 MET cc_start: 0.8880 (mmm) cc_final: 0.8533 (tpp) REVERT: E 489 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7863 (p) REVERT: E 617 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: F 430 MET cc_start: 0.8906 (tpp) cc_final: 0.8664 (tpp) REVERT: G 233 MET cc_start: 0.8872 (mmm) cc_final: 0.8641 (mmm) REVERT: G 257 MET cc_start: 0.8211 (mmp) cc_final: 0.7757 (mmp) REVERT: G 352 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7965 (p) REVERT: G 406 GLU cc_start: 0.8322 (tt0) cc_final: 0.7994 (tm-30) REVERT: G 440 MET cc_start: 0.7974 (ttm) cc_final: 0.7607 (mtp) REVERT: H 252 ARG cc_start: 0.6482 (mmt-90) cc_final: 0.5035 (mtm180) outliers start: 65 outliers final: 38 residues processed: 340 average time/residue: 0.2062 time to fit residues: 117.9856 Evaluate side-chains 300 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 592 ILE 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 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 499 LEU 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 489 VAL Chi-restraints excluded: chain E residue 567 SER 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 302 GLU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 417 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 G residue 570 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 292 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 190 optimal weight: 0.0010 chunk 195 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 397 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** C 161 HIS ** 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 = 0.3694 r_free = 0.3694 target = 0.101141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078351 restraints weight = 105330.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079741 restraints weight = 57935.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079964 restraints weight = 45654.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080496 restraints weight = 37518.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080522 restraints weight = 34116.435| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35229 Z= 0.169 Angle : 0.593 11.483 47657 Z= 0.285 Chirality : 0.043 0.275 5364 Planarity : 0.004 0.137 6206 Dihedral : 7.339 138.910 4843 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 1.93 % Allowed : 11.01 % Favored : 87.06 % 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: 1.21 (0.13), residues: 4330 helix: 1.72 (0.12), residues: 2106 sheet: -0.03 (0.21), residues: 615 loop : 0.03 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.016 0.001 TYR G 439 PHE 0.016 0.001 PHE D 275 TRP 0.012 0.001 TRP B 486 HIS 0.005 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (35219) covalent geometry : angle 0.59142 / 0.28 (47651) hydrogen bonds : bond 0.03302 / 2.20 ( 1622) hydrogen bonds : angle 4.36444 / 3.08 ( 4602) metal coordination : bond 0.03142 / 1.37 ( 8) metal coordination : angle 3.60293 / 3.32 ( 6) Misc. bond : bond 0.00058 / 0.03 ( 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 336 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 1.393 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: 0.7799 (tptp) cc_final: 0.7283 (tptt) REVERT: A 283 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 673 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7855 (ptpp) REVERT: B 571 ASP cc_start: 0.8446 (t0) cc_final: 0.7949 (t0) REVERT: B 621 MET cc_start: 0.8859 (tpp) cc_final: 0.8373 (tpp) REVERT: B 762 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: C 215 ASP cc_start: 0.8808 (t0) cc_final: 0.8481 (t0) REVERT: C 342 MET cc_start: 0.9216 (mmm) cc_final: 0.9010 (mmt) REVERT: C 437 MET cc_start: 0.8434 (tpp) cc_final: 0.8193 (tpp) REVERT: C 571 ASP cc_start: 0.8591 (t0) cc_final: 0.8214 (t0) REVERT: D 208 MET cc_start: 0.6318 (tpp) cc_final: 0.4961 (tpt) REVERT: D 493 ASP cc_start: 0.7978 (m-30) cc_final: 0.7543 (t70) REVERT: D 522 LYS cc_start: 0.8644 (tttt) cc_final: 0.8094 (tptm) REVERT: D 618 MET cc_start: 0.9151 (ttm) cc_final: 0.8932 (ttm) REVERT: D 621 MET cc_start: 0.7521 (tpt) cc_final: 0.6984 (tpt) REVERT: E 489 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (p) REVERT: E 617 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: F 430 MET cc_start: 0.8911 (tpp) cc_final: 0.8662 (tpp) REVERT: G 257 MET cc_start: 0.8305 (mmp) cc_final: 0.7758 (mmp) REVERT: G 352 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8064 (p) REVERT: G 406 GLU cc_start: 0.8448 (tt0) cc_final: 0.8220 (tt0) REVERT: G 440 MET cc_start: 0.8075 (ttm) cc_final: 0.7633 (mtp) REVERT: H 252 ARG cc_start: 0.6659 (mmt-90) cc_final: 0.5168 (mtm110) REVERT: H 293 ASP cc_start: 0.8643 (t0) cc_final: 0.8421 (t0) REVERT: L 351 GLU cc_start: 0.7395 (pm20) cc_final: 0.7108 (tp30) outliers start: 72 outliers final: 56 residues processed: 317 average time/residue: 0.1960 time to fit residues: 106.3737 Evaluate side-chains 315 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 592 ILE 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 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 319 ILE Chi-restraints excluded: chain D residue 345 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 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 617 GLU Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 302 GLU 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 G residue 570 GLN 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 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: 4.9990 chunk 251 optimal weight: 9.9990 chunk 214 optimal weight: 0.0670 chunk 231 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 290 optimal weight: 0.1980 chunk 366 optimal weight: 0.7980 chunk 378 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN G 289 GLN G 344 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082159 restraints weight = 105265.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081281 restraints weight = 59552.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082160 restraints weight = 54729.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.082675 restraints weight = 41248.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082868 restraints weight = 37775.017| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35229 Z= 0.101 Angle : 0.568 10.857 47657 Z= 0.269 Chirality : 0.042 0.246 5364 Planarity : 0.003 0.060 6206 Dihedral : 7.120 135.292 4843 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 1.56 % Allowed : 11.52 % Favored : 86.92 % 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: 1.78 (0.12), residues: 2097 sheet: 0.09 (0.21), residues: 623 loop : 0.08 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 369 TYR 0.013 0.001 TYR G 439 PHE 0.011 0.001 PHE H 300 TRP 0.010 0.001 TRP D 486 HIS 0.003 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (35219) covalent geometry : angle 0.56784 / 0.27 (47651) hydrogen bonds : bond 0.02830 / 1.88 ( 1622) hydrogen bonds : angle 4.18187 / 2.96 ( 4602) metal coordination : bond 0.01541 / 0.64 ( 8) metal coordination : angle 2.48978 / 1.89 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 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 332 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 1.041 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: 0.7889 (tptp) cc_final: 0.7487 (tptt) REVERT: A 673 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7930 (ptpp) REVERT: B 301 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 571 ASP cc_start: 0.8337 (t0) cc_final: 0.7841 (t0) REVERT: B 621 MET cc_start: 0.8728 (tpp) cc_final: 0.8429 (tpp) REVERT: B 762 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7483 (tmm) REVERT: C 56 MET cc_start: 0.3802 (ptp) cc_final: 0.3599 (ptp) REVERT: C 215 ASP cc_start: 0.8744 (t0) cc_final: 0.8465 (t0) REVERT: C 398 MET cc_start: 0.9018 (mmt) cc_final: 0.8798 (mmt) REVERT: C 437 MET cc_start: 0.8379 (tpp) cc_final: 0.8133 (tpp) REVERT: C 571 ASP cc_start: 0.8455 (t0) cc_final: 0.8090 (t0) REVERT: C 784 MET cc_start: 0.8344 (tmm) cc_final: 0.8010 (mmt) REVERT: D 208 MET cc_start: 0.6188 (tpp) cc_final: 0.4897 (tpt) REVERT: D 493 ASP cc_start: 0.8017 (m-30) cc_final: 0.7636 (t70) REVERT: D 522 LYS cc_start: 0.8525 (tttt) cc_final: 0.8024 (tptm) REVERT: D 618 MET cc_start: 0.9135 (ttm) cc_final: 0.8891 (ttm) REVERT: D 621 MET cc_start: 0.7370 (tpt) cc_final: 0.6914 (tpt) REVERT: E 223 MET cc_start: 0.8775 (mmm) cc_final: 0.8219 (tpp) REVERT: F 430 MET cc_start: 0.8825 (tpp) cc_final: 0.8600 (tpp) REVERT: G 205 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6163 (m90) REVERT: G 257 MET cc_start: 0.8172 (mmp) cc_final: 0.7884 (mmp) REVERT: G 406 GLU cc_start: 0.8315 (tt0) cc_final: 0.8072 (tt0) REVERT: G 440 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7550 (mtp) REVERT: H 252 ARG cc_start: 0.6699 (mmt-90) cc_final: 0.5067 (mtm180) REVERT: L 351 GLU cc_start: 0.7311 (pm20) cc_final: 0.7058 (tp30) outliers start: 58 outliers final: 43 residues processed: 319 average time/residue: 0.1872 time to fit residues: 101.8714 Evaluate side-chains 301 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 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 330 VAL Chi-restraints excluded: chain E residue 335 VAL 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 302 GLU Chi-restraints excluded: chain F residue 417 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 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 G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET 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 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: 0.5980 chunk 111 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 381 optimal weight: 2.9990 chunk 423 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.101421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078647 restraints weight = 105310.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080561 restraints weight = 58366.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080444 restraints weight = 46932.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080679 restraints weight = 38439.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080984 restraints weight = 34229.779| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35229 Z= 0.164 Angle : 0.604 11.108 47657 Z= 0.288 Chirality : 0.043 0.230 5364 Planarity : 0.004 0.060 6206 Dihedral : 7.088 135.392 4840 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 1.72 % Allowed : 11.95 % Favored : 86.33 % 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: 1.21 (0.13), residues: 4330 helix: 1.73 (0.12), residues: 2098 sheet: -0.04 (0.20), residues: 623 loop : 0.03 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.015 0.001 TYR G 439 PHE 0.024 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/Z covalent geometry : bond 0.00381 / 0.16 (35219) covalent geometry : angle 0.60259 / 0.29 (47651) hydrogen bonds : bond 0.03283 / 2.20 ( 1622) hydrogen bonds : angle 4.31213 / 3.05 ( 4602) metal coordination : bond 0.03137 / 1.34 ( 8) metal coordination : angle 3.19568 / 2.92 ( 6) Misc. bond : bond 0.00065 / 0.03 ( 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 320 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7769 (tptp) cc_final: 0.7350 (tptt) REVERT: A 673 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7856 (ptpp) REVERT: A 784 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6238 (mpp) REVERT: B 301 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 571 ASP cc_start: 0.8436 (t0) cc_final: 0.7939 (t0) REVERT: B 621 MET cc_start: 0.8850 (tpp) cc_final: 0.8371 (tpp) REVERT: B 762 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7599 (tmm) REVERT: C 215 ASP cc_start: 0.8851 (t0) cc_final: 0.8558 (t0) REVERT: C 398 MET cc_start: 0.9095 (mmt) cc_final: 0.8830 (mmt) REVERT: C 437 MET cc_start: 0.8458 (tpp) cc_final: 0.8221 (tpp) REVERT: C 571 ASP cc_start: 0.8563 (t0) cc_final: 0.8184 (t0) REVERT: C 784 MET cc_start: 0.8355 (tmm) cc_final: 0.7994 (mmt) REVERT: D 493 ASP cc_start: 0.7913 (m-30) cc_final: 0.7533 (t70) REVERT: D 522 LYS cc_start: 0.8587 (tttt) cc_final: 0.8018 (tptm) REVERT: D 621 MET cc_start: 0.7461 (tpt) cc_final: 0.6904 (tpt) REVERT: E 223 MET cc_start: 0.8936 (mmm) cc_final: 0.8624 (mmm) REVERT: E 489 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7991 (p) REVERT: E 514 THR cc_start: 0.8806 (m) cc_final: 0.8565 (p) REVERT: F 286 SER cc_start: 0.9316 (p) cc_final: 0.8781 (m) REVERT: F 430 MET cc_start: 0.8880 (tpp) cc_final: 0.8627 (tpp) REVERT: G 257 MET cc_start: 0.8303 (mmp) cc_final: 0.7841 (mmp) REVERT: G 352 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8054 (p) REVERT: G 406 GLU cc_start: 0.8344 (tt0) cc_final: 0.8104 (tt0) REVERT: G 440 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7613 (mtp) REVERT: H 252 ARG cc_start: 0.6827 (mmt-90) cc_final: 0.5106 (mtm110) REVERT: L 351 GLU cc_start: 0.7402 (pm20) cc_final: 0.7096 (tp30) outliers start: 64 outliers final: 54 residues processed: 300 average time/residue: 0.1852 time to fit residues: 95.1254 Evaluate side-chains 308 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 345 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 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 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU 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 G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain J residue 140 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 243 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 300 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 379 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 360 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077688 restraints weight = 105113.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079129 restraints weight = 57695.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079433 restraints weight = 47070.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079467 restraints weight = 39546.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079731 restraints weight = 35299.801| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 35229 Z= 0.190 Angle : 0.631 12.271 47657 Z= 0.303 Chirality : 0.043 0.222 5364 Planarity : 0.004 0.063 6206 Dihedral : 7.164 134.799 4840 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 1.83 % Allowed : 12.16 % 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: 1.07 (0.13), residues: 4330 helix: 1.60 (0.12), residues: 2104 sheet: -0.07 (0.21), residues: 613 loop : -0.06 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 323 TYR 0.017 0.001 TYR G 439 PHE 0.023 0.001 PHE G 509 TRP 0.014 0.001 TRP B 486 HIS 0.005 0.001 HIS G 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (35219) covalent geometry : angle 0.63007 / 0.30 (47651) hydrogen bonds : bond 0.03463 / 2.32 ( 1622) hydrogen bonds : angle 4.43823 / 3.14 ( 4602) metal coordination : bond 0.03688 / 1.58 ( 8) metal coordination : angle 3.79709 / 3.38 ( 6) Misc. bond : bond 0.00074 / 0.04 ( 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 323 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7792 (tptp) cc_final: 0.7342 (tptt) REVERT: A 437 MET cc_start: 0.7938 (tmm) cc_final: 0.7532 (tpt) REVERT: A 673 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7887 (ptpp) REVERT: A 784 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6317 (mpp) REVERT: B 223 MET cc_start: 0.9222 (tpp) cc_final: 0.8874 (tpt) REVERT: B 571 ASP cc_start: 0.8450 (t0) cc_final: 0.7961 (t0) REVERT: B 621 MET cc_start: 0.8927 (tpp) cc_final: 0.8471 (tpp) REVERT: B 762 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7595 (tmm) REVERT: C 215 ASP cc_start: 0.8863 (t0) cc_final: 0.8593 (t0) REVERT: C 437 MET cc_start: 0.8453 (tpp) cc_final: 0.8206 (tpp) REVERT: C 571 ASP cc_start: 0.8607 (t0) cc_final: 0.8232 (t0) REVERT: D 208 MET cc_start: 0.6377 (tpp) cc_final: 0.4884 (tpt) REVERT: D 493 ASP cc_start: 0.7974 (m-30) cc_final: 0.7551 (t70) REVERT: D 522 LYS cc_start: 0.8588 (tttt) cc_final: 0.7984 (tptm) REVERT: D 621 MET cc_start: 0.7491 (tpt) cc_final: 0.6945 (tpt) REVERT: E 489 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7984 (p) REVERT: E 514 THR cc_start: 0.8860 (m) cc_final: 0.8606 (p) REVERT: F 286 SER cc_start: 0.9174 (p) cc_final: 0.8882 (m) REVERT: F 430 MET cc_start: 0.8902 (tpp) cc_final: 0.8643 (tpp) REVERT: G 257 MET cc_start: 0.8304 (mmp) cc_final: 0.7810 (mmp) REVERT: G 352 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8153 (p) REVERT: G 406 GLU cc_start: 0.8293 (tt0) cc_final: 0.8056 (tt0) REVERT: G 440 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: H 252 ARG cc_start: 0.6834 (mmt-90) cc_final: 0.5001 (mtm110) REVERT: L 348 LYS cc_start: 0.6349 (mmmt) cc_final: 0.5782 (mtmm) REVERT: L 351 GLU cc_start: 0.7358 (pm20) cc_final: 0.7150 (tp30) outliers start: 68 outliers final: 56 residues processed: 306 average time/residue: 0.1882 time to fit residues: 98.5199 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 : 1.276 ------------------------------------------------------------------------------- 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 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 345 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 489 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU 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 G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN 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: 10.0000 chunk 249 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 338 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 374 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079874 restraints weight = 105996.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079186 restraints weight = 60463.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080161 restraints weight = 57185.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080231 restraints weight = 42595.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081317 restraints weight = 38699.140| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35229 Z= 0.165 Angle : 0.628 13.220 47657 Z= 0.299 Chirality : 0.043 0.223 5364 Planarity : 0.004 0.063 6206 Dihedral : 7.130 133.862 4840 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 1.69 % Allowed : 12.41 % 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: 1.07 (0.13), residues: 4330 helix: 1.61 (0.12), residues: 2098 sheet: -0.07 (0.21), residues: 610 loop : -0.06 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 259 TYR 0.016 0.001 TYR G 439 PHE 0.022 0.001 PHE G 509 TRP 0.014 0.001 TRP B 486 HIS 0.004 0.001 HIS G 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (35219) covalent geometry : angle 0.62632 / 0.30 (47651) hydrogen bonds : bond 0.03329 / 2.23 ( 1622) hydrogen bonds : angle 4.40505 / 3.12 ( 4602) metal coordination : bond 0.03097 / 1.31 ( 8) metal coordination : angle 3.92265 / 3.51 ( 6) Misc. bond : bond 0.00054 / 0.03 ( 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 318 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7856 (tptp) cc_final: 0.7446 (tptt) REVERT: A 437 MET cc_start: 0.7932 (tmm) cc_final: 0.7591 (tpt) REVERT: A 673 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7856 (ptpp) REVERT: A 784 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: B 223 MET cc_start: 0.9138 (tpp) cc_final: 0.8802 (tpt) REVERT: B 301 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 571 ASP cc_start: 0.8336 (t0) cc_final: 0.7842 (t0) REVERT: B 621 MET cc_start: 0.8884 (tpp) cc_final: 0.8472 (tpp) REVERT: B 762 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7555 (tmm) REVERT: C 215 ASP cc_start: 0.8801 (t0) cc_final: 0.8567 (t0) REVERT: C 398 MET cc_start: 0.8992 (mmt) cc_final: 0.8766 (mmt) REVERT: C 437 MET cc_start: 0.8449 (tpp) cc_final: 0.8176 (tpp) REVERT: C 571 ASP cc_start: 0.8485 (t0) cc_final: 0.8101 (t0) REVERT: C 784 MET cc_start: 0.8407 (tmm) cc_final: 0.7997 (mmt) REVERT: D 208 MET cc_start: 0.6511 (tpp) cc_final: 0.4990 (tpt) REVERT: D 493 ASP cc_start: 0.7943 (m-30) cc_final: 0.7545 (t70) REVERT: D 522 LYS cc_start: 0.8528 (tttt) cc_final: 0.7938 (tptm) REVERT: D 621 MET cc_start: 0.7427 (tpt) cc_final: 0.6987 (tpt) REVERT: E 489 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7976 (p) REVERT: E 514 THR cc_start: 0.8847 (m) cc_final: 0.8585 (p) REVERT: F 286 SER cc_start: 0.9202 (p) cc_final: 0.8862 (m) REVERT: F 430 MET cc_start: 0.8840 (tpp) cc_final: 0.8597 (tpp) REVERT: G 257 MET cc_start: 0.8194 (mmp) cc_final: 0.7843 (mmp) REVERT: G 352 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8156 (p) REVERT: G 406 GLU cc_start: 0.8246 (tt0) cc_final: 0.8033 (tt0) REVERT: G 440 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7505 (mtp) REVERT: H 252 ARG cc_start: 0.7049 (mmt-90) cc_final: 0.5141 (mtm110) REVERT: L 348 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6109 (ptpt) REVERT: L 351 GLU cc_start: 0.7367 (pm20) cc_final: 0.7165 (tp30) outliers start: 63 outliers final: 56 residues processed: 301 average time/residue: 0.1953 time to fit residues: 100.4036 Evaluate side-chains 312 residues out of total 3724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 345 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 709 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU 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 G residue 570 GLN Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 140 GLN 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: 0.9990 chunk 25 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080151 restraints weight = 105532.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079358 restraints weight = 60535.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080367 restraints weight = 57088.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080397 restraints weight = 43754.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080870 restraints weight = 39712.410| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2974 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= 0.154 Angle : 0.621 12.682 47657 Z= 0.295 Chirality : 0.043 0.313 5364 Planarity : 0.004 0.062 6206 Dihedral : 7.090 132.897 4840 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 1.75 % Allowed : 12.41 % Favored : 85.85 % 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: 1.08 (0.13), residues: 4330 helix: 1.62 (0.12), residues: 2098 sheet: -0.04 (0.21), residues: 606 loop : -0.05 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 648 TYR 0.015 0.001 TYR G 439 PHE 0.021 0.001 PHE G 509 TRP 0.012 0.001 TRP D 486 HIS 0.004 0.001 HIS G 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (35219) covalent geometry : angle 0.61937 / 0.29 (47651) hydrogen bonds : bond 0.03251 / 2.18 ( 1622) hydrogen bonds : angle 4.38786 / 3.11 ( 4602) metal coordination : bond 0.02931 / 1.24 ( 8) metal coordination : angle 3.91936 / 3.46 ( 6) Misc. bond : bond 0.00053 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.01 seconds wall clock time: 95 minutes 47.95 seconds (5747.95 seconds total)