Starting phenix.real_space_refine on Tue Oct 27 04:44:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxd_30905/10_2026/7dxd_30905.cif" } resolution = 3.9 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= 0.013 sd= 0.083 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 Ca 4 9.91 5 Zn 4 6.06 5 S 132 5.16 5 C 15424 2.51 5 N 3792 2.21 5 O 4272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23628 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5870 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1328 SG CYS A 182 86.403 24.516 78.918 1.00143.63 S ATOM 1343 SG CYS A 184 88.739 23.851 76.056 1.00140.89 S ATOM 1361 SG CYS A 187 87.488 27.317 76.638 1.00138.90 S ATOM 7198 SG CYS B 182 98.798 86.400 78.920 1.00143.63 S ATOM 7213 SG CYS B 184 99.463 88.736 76.058 1.00140.89 S ATOM 7231 SG CYS B 187 95.997 87.485 76.640 1.00138.90 S ATOM 13068 SG CYS C 182 24.519 36.912 78.913 1.00143.63 S ATOM 13083 SG CYS C 184 23.854 34.576 76.051 1.00140.89 S ATOM 13101 SG CYS C 187 27.320 35.827 76.634 1.00138.90 S ATOM 18938 SG CYS D 182 36.914 98.795 78.915 1.00143.63 S ATOM 18953 SG CYS D 184 34.579 99.460 76.053 1.00140.89 S ATOM 18971 SG CYS D 187 35.830 95.994 76.635 1.00138.90 S Time building chain proxies: 6.62, per 1000 atoms: 0.28 Number of scatterers: 23628 At special positions: 0 Unit cell: (124.355, 124.355, 167.2, 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 4 29.99 Ca 4 19.99 S 132 16.00 O 4272 8.00 N 3792 7.00 C 15424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 934.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 178 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 182 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 184 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 187 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 178 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 182 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 184 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 187 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" ND1 HIS C 178 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 182 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 184 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 187 " pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" ND1 HIS D 178 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 182 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 184 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 187 " Number of angles added : 12 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 39 through 50 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.928A pdb=" N GLN A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.971A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 358 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 423 through 448 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 539 through 548 removed outlier: 4.149A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.770A pdb=" N SER A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 622 " --> pdb=" O VAL A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 622' Processing helix chain 'A' and resid 628 through 663 Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 788 through 824 removed outlier: 3.713A pdb=" N ILE A 795 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.928A pdb=" N GLN B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.970A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG B 330 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 358 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 423 through 448 Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU B 545 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Proline residue: B 546 - end of helix Processing helix chain 'B' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.769A pdb=" N SER B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 628 through 663 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 761 through 784 Processing helix chain 'B' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 39 through 50 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 83 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.929A pdb=" N GLN C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.970A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 240 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.601A pdb=" N ARG C 330 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 358 Proline residue: C 349 - end of helix Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 423 through 448 Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.644A pdb=" N LEU C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 538 Processing helix chain 'C' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU C 545 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Proline residue: C 546 - end of helix Processing helix chain 'C' and resid 551 through 588 removed outlier: 4.682A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.768A pdb=" N SER C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 622 " --> pdb=" O VAL C 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 618 through 622' Processing helix chain 'C' and resid 628 through 663 Processing helix chain 'C' and resid 669 through 683 Processing helix chain 'C' and resid 761 through 784 Processing helix chain 'C' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 39 through 50 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 83 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 124 through 131 removed outlier: 3.929A pdb=" N GLN D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.971A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.613A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.600A pdb=" N ARG D 330 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 358 Proline residue: D 349 - end of helix Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 369 through 392 removed outlier: 3.805A pdb=" N ALA D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 423 through 448 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.643A pdb=" N LEU D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 538 Processing helix chain 'D' and resid 539 through 548 removed outlier: 4.150A pdb=" N LEU D 545 " --> pdb=" O ALA D 542 " (cutoff:3.500A) Proline residue: D 546 - end of helix Processing helix chain 'D' and resid 551 through 588 removed outlier: 4.683A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.769A pdb=" N SER D 621 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 622 " --> pdb=" O VAL D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 622' Processing helix chain 'D' and resid 628 through 663 Processing helix chain 'D' and resid 669 through 683 Processing helix chain 'D' and resid 761 through 784 Processing helix chain 'D' and resid 788 through 824 removed outlier: 3.712A pdb=" N ILE D 795 " --> pdb=" O GLU D 791 " (cutoff:3.500A) 1600 hydrogen bonds defined for protein. 4740 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: 4.39 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7376 1.34 - 1.47: 5776 1.47 - 1.59: 10776 1.59 - 1.72: 4 1.72 - 1.84: 216 Bond restraints: 24148 Sorted by residual: bond pdb=" CAY Y01 B 901 " pdb=" OAW Y01 B 901 " ideal model delta sigma weight residual 1.332 1.466 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" CAY Y01 A 901 " pdb=" OAW Y01 A 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAY Y01 C 901 " pdb=" OAW Y01 C 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAY Y01 D 901 " pdb=" OAW Y01 D 901 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CAX Y01 B 901 " pdb=" OAH Y01 B 901 " ideal model delta sigma weight residual 1.248 1.330 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 24143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 32179 2.03 - 4.06: 424 4.06 - 6.09: 89 6.09 - 8.12: 28 8.12 - 10.15: 4 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C LEU B 24 " pdb=" CA LEU B 24 " pdb=" CB LEU B 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU A 24 " pdb=" CA LEU A 24 " pdb=" CB LEU A 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU C 24 " pdb=" CA LEU C 24 " pdb=" CB LEU C 24 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" C LEU D 24 " pdb=" CA LEU D 24 " pdb=" CB LEU D 24 " ideal model delta sigma weight residual 116.54 110.58 5.96 1.15e+00 7.56e-01 2.68e+01 angle pdb=" CA LEU D 24 " pdb=" C LEU D 24 " pdb=" N THR D 25 " ideal model delta sigma weight residual 119.52 115.45 4.07 7.90e-01 1.60e+00 2.65e+01 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 13064 16.23 - 32.46: 1044 32.46 - 48.69: 208 48.69 - 64.92: 92 64.92 - 81.15: 24 Dihedral angle restraints: 14432 sinusoidal: 5792 harmonic: 8640 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ILE A 174 " pdb=" C ILE A 174 " pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ILE C 174 " pdb=" C ILE C 174 " pdb=" N GLU C 175 " pdb=" CA GLU C 175 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 14429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3268 0.058 - 0.116: 439 0.116 - 0.173: 17 0.173 - 0.231: 4 0.231 - 0.289: 4 Chirality restraints: 3732 Sorted by residual: chirality pdb=" CB ILE A 655 " pdb=" CA ILE A 655 " pdb=" CG1 ILE A 655 " pdb=" CG2 ILE A 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE B 655 " pdb=" CA ILE B 655 " pdb=" CG1 ILE B 655 " pdb=" CG2 ILE B 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE C 655 " pdb=" CA ILE C 655 " pdb=" CG1 ILE C 655 " pdb=" CG2 ILE C 655 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 3729 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 656 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA B 656 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA B 656 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 657 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 656 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA C 656 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA C 656 " 0.011 2.00e-02 2.50e+03 pdb=" N MET C 657 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 656 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ALA A 656 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 656 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 657 " 0.010 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5500 2.79 - 3.32: 23849 3.32 - 3.84: 39439 3.84 - 4.37: 45856 4.37 - 4.90: 77826 Nonbonded interactions: 192470 Sorted by model distance: nonbonded pdb=" O TYR C 214 " pdb=" OG SER C 218 " model vdw 2.260 3.040 nonbonded pdb=" O TYR B 214 " pdb=" OG SER B 218 " model vdw 2.260 3.040 nonbonded pdb=" O TYR D 214 " pdb=" OG SER D 218 " model vdw 2.260 3.040 nonbonded pdb=" O TYR A 214 " pdb=" OG SER A 218 " model vdw 2.260 3.040 nonbonded pdb=" NZ LYS B 306 " pdb=" OE2 GLU B 672 " model vdw 2.299 3.120 ... (remaining 192465 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.650 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.460 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.005 0.166 24164 Z= 0.232 Angle : 0.678 14.678 32736 Z= 0.346 Chirality : 0.039 0.289 3732 Planarity : 0.004 0.035 4076 Dihedral : 13.455 81.154 8824 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 6.27 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 2880 helix: 0.09 (0.10), residues: 2044 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 44 TYR 0.012 0.001 TYR C 639 PHE 0.009 0.001 PHE C 381 TRP 0.010 0.001 TRP C 611 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (24148) covalent geometry : angle 0.62860 / 0.34 (32724) hydrogen bonds : bond 0.12762 / 8.22 ( 1600) hydrogen bonds : angle 4.60219 / 3.30 ( 4740) metal coordination : bond 0.13191 / 8.74 ( 16) metal coordination : angle 13.28790 / 9.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 369 time to evaluate : 0.918 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 464 MET cc_start: 0.9152 (ttp) cc_final: 0.8622 (tmm) REVERT: B 15 PHE cc_start: 0.6702 (m-10) cc_final: 0.6493 (m-80) REVERT: B 464 MET cc_start: 0.9151 (ttp) cc_final: 0.8625 (tmm) REVERT: C 464 MET cc_start: 0.9151 (ttp) cc_final: 0.8627 (tmm) REVERT: D 15 PHE cc_start: 0.6710 (m-10) cc_final: 0.6496 (m-80) REVERT: D 464 MET cc_start: 0.9152 (ttp) cc_final: 0.8625 (tmm) outliers start: 32 outliers final: 0 residues processed: 393 average time/residue: 0.1475 time to fit residues: 94.2019 Evaluate side-chains 178 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 659 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN C 659 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D 659 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.051451 restraints weight = 96918.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.053339 restraints weight = 52653.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054696 restraints weight = 35254.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055558 restraints weight = 26782.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056135 restraints weight = 22259.155| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24164 Z= 0.175 Angle : 0.603 8.750 32736 Z= 0.313 Chirality : 0.039 0.158 3732 Planarity : 0.004 0.043 4076 Dihedral : 4.616 52.129 3200 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 9.09 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.10 (0.15), residues: 2880 helix: 1.46 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.016 0.001 TYR B 138 PHE 0.022 0.002 PHE A 15 TRP 0.014 0.002 TRP B 322 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (24148) covalent geometry : angle 0.60239 / 0.31 (32724) hydrogen bonds : bond 0.04896 / 3.31 ( 1600) hydrogen bonds : angle 3.92599 / 2.84 ( 4740) metal coordination : bond 0.00617 / 0.46 ( 16) metal coordination : angle 1.86858 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.687 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 169 MET cc_start: 0.8823 (mmm) cc_final: 0.8564 (mmm) REVERT: A 252 MET cc_start: 0.8430 (tpp) cc_final: 0.8185 (tpp) REVERT: A 464 MET cc_start: 0.9168 (ttp) cc_final: 0.8792 (tmm) REVERT: A 572 PHE cc_start: 0.8407 (t80) cc_final: 0.6245 (t80) REVERT: B 169 MET cc_start: 0.8829 (mmm) cc_final: 0.8574 (mmm) REVERT: B 252 MET cc_start: 0.8426 (tpp) cc_final: 0.8182 (tpp) REVERT: B 464 MET cc_start: 0.9172 (ttp) cc_final: 0.8791 (tmm) REVERT: B 572 PHE cc_start: 0.8402 (t80) cc_final: 0.6238 (t80) REVERT: C 169 MET cc_start: 0.8822 (mmm) cc_final: 0.8563 (mmm) REVERT: C 464 MET cc_start: 0.9163 (ttp) cc_final: 0.8787 (tmm) REVERT: C 572 PHE cc_start: 0.8407 (t80) cc_final: 0.6263 (t80) REVERT: C 652 ASN cc_start: 0.8834 (t0) cc_final: 0.8570 (t0) REVERT: D 169 MET cc_start: 0.8820 (mmm) cc_final: 0.8561 (mmm) REVERT: D 252 MET cc_start: 0.8411 (tpp) cc_final: 0.8169 (tpp) REVERT: D 464 MET cc_start: 0.9171 (ttp) cc_final: 0.8789 (tmm) REVERT: D 572 PHE cc_start: 0.8406 (t80) cc_final: 0.6254 (t80) REVERT: D 652 ASN cc_start: 0.8824 (t0) cc_final: 0.8556 (t0) outliers start: 64 outliers final: 41 residues processed: 230 average time/residue: 0.1273 time to fit residues: 50.7382 Evaluate side-chains 174 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [218, 226, 280, 38, 16, 287, 223, 228, 155, 279, 119] chunk 218 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 280 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052148 restraints weight = 96541.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.054076 restraints weight = 52277.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055363 restraints weight = 34976.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056323 restraints weight = 26684.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057013 restraints weight = 21978.822| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24164 Z= 0.117 Angle : 0.531 7.472 32736 Z= 0.272 Chirality : 0.038 0.126 3732 Planarity : 0.004 0.040 4076 Dihedral : 4.403 51.761 3200 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.59 % Allowed : 10.11 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.86 (0.15), residues: 2880 helix: 2.05 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 330 TYR 0.011 0.001 TYR B 37 PHE 0.018 0.001 PHE C 572 TRP 0.010 0.001 TRP C 322 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (24148) covalent geometry : angle 0.53015 / 0.27 (32724) hydrogen bonds : bond 0.04413 / 2.99 ( 1600) hydrogen bonds : angle 3.58281 / 2.59 ( 4740) metal coordination : bond 0.00347 / 0.25 ( 16) metal coordination : angle 1.67580 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 138 time to evaluate : 0.932 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: A 169 MET cc_start: 0.8798 (mmm) cc_final: 0.8573 (mmm) REVERT: A 252 MET cc_start: 0.8549 (tpp) cc_final: 0.8345 (tpp) REVERT: A 464 MET cc_start: 0.9121 (ttp) cc_final: 0.8536 (tmm) REVERT: A 572 PHE cc_start: 0.8507 (t80) cc_final: 0.7109 (t80) REVERT: B 61 MET cc_start: 0.8565 (mmp) cc_final: 0.8359 (tpp) REVERT: B 252 MET cc_start: 0.8552 (tpp) cc_final: 0.8344 (tpp) REVERT: B 464 MET cc_start: 0.9125 (ttp) cc_final: 0.8546 (tmm) REVERT: B 572 PHE cc_start: 0.8500 (t80) cc_final: 0.7103 (t80) REVERT: B 583 MET cc_start: 0.8696 (mtt) cc_final: 0.8375 (mtp) REVERT: B 782 LYS cc_start: 0.9413 (tppt) cc_final: 0.9126 (tppt) REVERT: C 464 MET cc_start: 0.9122 (ttp) cc_final: 0.8541 (tmm) REVERT: C 572 PHE cc_start: 0.8507 (t80) cc_final: 0.7114 (t80) REVERT: C 583 MET cc_start: 0.8697 (mtt) cc_final: 0.8370 (mtp) REVERT: D 464 MET cc_start: 0.9126 (ttp) cc_final: 0.8547 (tmm) REVERT: D 572 PHE cc_start: 0.8505 (t80) cc_final: 0.7104 (t80) REVERT: D 583 MET cc_start: 0.8687 (mtt) cc_final: 0.8367 (mtp) REVERT: D 782 LYS cc_start: 0.9453 (tppt) cc_final: 0.9224 (tppt) outliers start: 66 outliers final: 24 residues processed: 199 average time/residue: 0.1313 time to fit residues: 44.9178 Evaluate side-chains 162 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [218, 121, 80, 185, 103, 125, 1, 94, 22, 276, 181] chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 103 optimal weight: 0.0010 chunk 125 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050575 restraints weight = 97307.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052423 restraints weight = 53362.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053687 restraints weight = 35966.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054646 restraints weight = 27497.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055201 restraints weight = 22631.346| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24164 Z= 0.146 Angle : 0.533 8.827 32736 Z= 0.275 Chirality : 0.037 0.132 3732 Planarity : 0.004 0.040 4076 Dihedral : 4.321 48.367 3200 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 11.17 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.25 (0.16), residues: 2880 helix: 2.33 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -1.03 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 266 TYR 0.012 0.001 TYR B 37 PHE 0.021 0.001 PHE B 568 TRP 0.013 0.001 TRP B 432 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (24148) covalent geometry : angle 0.53282 / 0.28 (32724) hydrogen bonds : bond 0.04384 / 2.96 ( 1600) hydrogen bonds : angle 3.54926 / 2.58 ( 4740) metal coordination : bond 0.00275 / 0.18 ( 16) metal coordination : angle 1.45668 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9104 (ttp) cc_final: 0.8595 (tmm) REVERT: B 464 MET cc_start: 0.9108 (ttp) cc_final: 0.8588 (tmm) REVERT: B 583 MET cc_start: 0.8759 (mtt) cc_final: 0.8476 (mtp) REVERT: C 464 MET cc_start: 0.9108 (ttp) cc_final: 0.8592 (tmm) REVERT: C 583 MET cc_start: 0.8760 (mtt) cc_final: 0.8478 (mtp) REVERT: D 169 MET cc_start: 0.8815 (mmm) cc_final: 0.8613 (mmm) REVERT: D 464 MET cc_start: 0.9109 (ttp) cc_final: 0.8589 (tmm) REVERT: D 583 MET cc_start: 0.8749 (mtt) cc_final: 0.8468 (mtp) REVERT: D 782 LYS cc_start: 0.9442 (tppt) cc_final: 0.9214 (tppt) outliers start: 52 outliers final: 33 residues processed: 185 average time/residue: 0.1260 time to fit residues: 40.6090 Evaluate side-chains 158 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [106, 142, 64, 171, 291, 91, 284, 103, 101, 183, 174] chunk 106 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050005 restraints weight = 97258.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051724 restraints weight = 54833.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052957 restraints weight = 37667.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053802 restraints weight = 28965.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054352 restraints weight = 24191.372| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24164 Z= 0.149 Angle : 0.514 7.953 32736 Z= 0.269 Chirality : 0.038 0.132 3732 Planarity : 0.004 0.040 4076 Dihedral : 4.247 44.565 3200 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.96 % Allowed : 12.03 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.45 (0.16), residues: 2880 helix: 2.46 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -0.88 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.012 0.001 TYR C 37 PHE 0.027 0.001 PHE D 568 TRP 0.012 0.002 TRP C 322 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (24148) covalent geometry : angle 0.51375 / 0.27 (32724) hydrogen bonds : bond 0.04364 / 2.95 ( 1600) hydrogen bonds : angle 3.52777 / 2.56 ( 4740) metal coordination : bond 0.00342 / 0.24 ( 16) metal coordination : angle 1.39684 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.9551 (mm) cc_final: 0.9286 (tt) REVERT: A 464 MET cc_start: 0.9114 (ttp) cc_final: 0.8596 (tmm) REVERT: B 274 ILE cc_start: 0.9544 (mm) cc_final: 0.9285 (tt) REVERT: B 464 MET cc_start: 0.9109 (ttp) cc_final: 0.8591 (tmm) REVERT: C 274 ILE cc_start: 0.9547 (mm) cc_final: 0.9291 (tt) REVERT: C 464 MET cc_start: 0.9113 (ttp) cc_final: 0.8595 (tmm) REVERT: D 169 MET cc_start: 0.8748 (mmm) cc_final: 0.8513 (mmm) REVERT: D 274 ILE cc_start: 0.9543 (mm) cc_final: 0.9291 (tt) REVERT: D 464 MET cc_start: 0.9113 (ttp) cc_final: 0.8592 (tmm) REVERT: D 782 LYS cc_start: 0.9410 (tppt) cc_final: 0.9200 (tppt) outliers start: 50 outliers final: 28 residues processed: 180 average time/residue: 0.1281 time to fit residues: 39.9664 Evaluate side-chains 152 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [131, 31, 244, 61, 267, 123, 271, 215, 283, 19, 243] chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 215 optimal weight: 0.0570 chunk 283 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050722 restraints weight = 97309.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052505 restraints weight = 54332.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053803 restraints weight = 36848.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054549 restraints weight = 28350.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055236 restraints weight = 23860.630| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24164 Z= 0.108 Angle : 0.487 7.395 32736 Z= 0.254 Chirality : 0.037 0.126 3732 Planarity : 0.004 0.039 4076 Dihedral : 4.178 43.972 3200 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.68 % Allowed : 12.70 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.64 (0.16), residues: 2880 helix: 2.58 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -0.76 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 475 TYR 0.010 0.001 TYR A 37 PHE 0.032 0.001 PHE D 568 TRP 0.010 0.001 TRP C 322 HIS 0.002 0.000 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (24148) covalent geometry : angle 0.48682 / 0.25 (32724) hydrogen bonds : bond 0.04039 / 2.73 ( 1600) hydrogen bonds : angle 3.40945 / 2.47 ( 4740) metal coordination : bond 0.00169 / 0.11 ( 16) metal coordination : angle 1.04734 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8602 (tmm) REVERT: A 646 MET cc_start: 0.8825 (tpp) cc_final: 0.8546 (tpp) REVERT: B 464 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8598 (tmm) REVERT: B 646 MET cc_start: 0.8837 (tpp) cc_final: 0.8550 (tpp) REVERT: C 464 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8603 (tmm) REVERT: C 646 MET cc_start: 0.8800 (tpp) cc_final: 0.8531 (tpp) REVERT: D 169 MET cc_start: 0.8788 (mmm) cc_final: 0.8529 (mmm) REVERT: D 464 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8594 (tmm) REVERT: D 646 MET cc_start: 0.8796 (tpp) cc_final: 0.8519 (tpp) outliers start: 43 outliers final: 32 residues processed: 171 average time/residue: 0.1292 time to fit residues: 38.5443 Evaluate side-chains 165 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [255, 51, 8, 114, 21, 26, 38, 111, 44, 24, 190] chunk 255 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051046 restraints weight = 98301.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052825 restraints weight = 54635.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054078 restraints weight = 37035.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054880 restraints weight = 28499.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055501 restraints weight = 23892.677| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24164 Z= 0.107 Angle : 0.486 7.843 32736 Z= 0.252 Chirality : 0.037 0.126 3732 Planarity : 0.004 0.038 4076 Dihedral : 4.083 43.940 3200 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.04 % Allowed : 12.89 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.73 (0.16), residues: 2880 helix: 2.63 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -0.66 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 330 TYR 0.010 0.001 TYR D 37 PHE 0.032 0.001 PHE D 568 TRP 0.011 0.001 TRP A 322 HIS 0.002 0.000 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (24148) covalent geometry : angle 0.48590 / 0.25 (32724) hydrogen bonds : bond 0.03946 / 2.67 ( 1600) hydrogen bonds : angle 3.37084 / 2.44 ( 4740) metal coordination : bond 0.00161 / 0.11 ( 16) metal coordination : angle 0.97797 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8571 (tmm) REVERT: B 16 MET cc_start: 0.6890 (mmp) cc_final: 0.6679 (mmp) REVERT: B 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: C 464 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8566 (tmm) REVERT: C 659 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.7975 (m110) REVERT: D 169 MET cc_start: 0.8752 (mmm) cc_final: 0.8485 (mmm) REVERT: D 464 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8567 (tmm) outliers start: 52 outliers final: 37 residues processed: 176 average time/residue: 0.1287 time to fit residues: 39.3712 Evaluate side-chains 173 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 659 ASN Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [194, 160, 80, 83, 137, 54, 263, 24, 57, 182, 278] chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 83 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051007 restraints weight = 98662.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052772 restraints weight = 55000.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053985 restraints weight = 37540.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054784 restraints weight = 28958.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055419 restraints weight = 24296.171| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24164 Z= 0.112 Angle : 0.492 7.282 32736 Z= 0.256 Chirality : 0.037 0.127 3732 Planarity : 0.004 0.039 4076 Dihedral : 4.064 43.663 3200 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.96 % Allowed : 13.24 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.77 (0.16), residues: 2880 helix: 2.64 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -0.59 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.010 0.001 TYR D 37 PHE 0.035 0.001 PHE A 568 TRP 0.011 0.001 TRP D 322 HIS 0.002 0.000 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (24148) covalent geometry : angle 0.49184 / 0.26 (32724) hydrogen bonds : bond 0.03954 / 2.67 ( 1600) hydrogen bonds : angle 3.41886 / 2.48 ( 4740) metal coordination : bond 0.00198 / 0.13 ( 16) metal coordination : angle 0.99977 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8585 (tmm) REVERT: B 464 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8586 (tmm) REVERT: C 464 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8579 (tmm) REVERT: D 169 MET cc_start: 0.8750 (mmm) cc_final: 0.8492 (mmm) REVERT: D 464 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8587 (tmm) outliers start: 50 outliers final: 36 residues processed: 170 average time/residue: 0.1263 time to fit residues: 37.3979 Evaluate side-chains 175 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [173, 211, 146, 86, 147, 152, 27, 212, 230, 208, 231] chunk 173 optimal weight: 0.0040 chunk 211 optimal weight: 0.7980 chunk 146 optimal weight: 30.0000 chunk 86 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051185 restraints weight = 98901.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052971 restraints weight = 55009.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054228 restraints weight = 37398.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055042 restraints weight = 28697.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055565 restraints weight = 23986.696| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24164 Z= 0.105 Angle : 0.492 7.474 32736 Z= 0.256 Chirality : 0.037 0.212 3732 Planarity : 0.004 0.039 4076 Dihedral : 3.996 44.524 3200 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.61 % Allowed : 13.60 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.67 (0.16), residues: 2880 helix: 2.58 (0.11), residues: 2172 sheet: None (None), residues: 0 loop : -0.92 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 560 TYR 0.010 0.001 TYR D 642 PHE 0.036 0.001 PHE C 568 TRP 0.027 0.001 TRP B 432 HIS 0.002 0.000 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (24148) covalent geometry : angle 0.49147 / 0.26 (32724) hydrogen bonds : bond 0.03816 / 2.59 ( 1600) hydrogen bonds : angle 3.38157 / 2.46 ( 4740) metal coordination : bond 0.00136 / 0.09 ( 16) metal coordination : angle 0.88600 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8558 (tmm) REVERT: B 464 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8560 (tmm) REVERT: C 464 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8555 (tmm) REVERT: D 169 MET cc_start: 0.8768 (mmm) cc_final: 0.8509 (mmm) REVERT: D 464 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8561 (tmm) outliers start: 41 outliers final: 28 residues processed: 166 average time/residue: 0.1329 time to fit residues: 38.0670 Evaluate side-chains 165 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [113, 174, 186, 283, 290, 159, 46, 234, 81, 16, 78] chunk 113 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050524 restraints weight = 98668.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052271 restraints weight = 55099.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053500 restraints weight = 37501.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054344 restraints weight = 28876.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054862 restraints weight = 24021.933| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24164 Z= 0.124 Angle : 0.519 8.202 32736 Z= 0.268 Chirality : 0.037 0.239 3732 Planarity : 0.004 0.039 4076 Dihedral : 4.012 43.706 3200 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.37 % Allowed : 14.07 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.70 (0.16), residues: 2880 helix: 2.57 (0.11), residues: 2176 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.010 0.001 TYR C 37 PHE 0.034 0.001 PHE A 568 TRP 0.016 0.001 TRP A 432 HIS 0.002 0.000 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24148) covalent geometry : angle 0.51892 / 0.27 (32724) hydrogen bonds : bond 0.03928 / 2.66 ( 1600) hydrogen bonds : angle 3.43434 / 2.50 ( 4740) metal coordination : bond 0.00303 / 0.22 ( 16) metal coordination : angle 1.00987 / 0.88 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8607 (tmm) REVERT: B 464 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8610 (tmm) REVERT: C 464 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8601 (tmm) REVERT: D 46 MET cc_start: 0.8743 (mtp) cc_final: 0.8517 (mtp) REVERT: D 169 MET cc_start: 0.8776 (mmm) cc_final: 0.8507 (mmm) REVERT: D 464 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8610 (tmm) outliers start: 35 outliers final: 28 residues processed: 161 average time/residue: 0.1292 time to fit residues: 36.1425 Evaluate side-chains 165 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 791 GLU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 795 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: [220, 227, 246, 226, 19, 36, 75, 26, 62, 148, 56] chunk 220 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 75 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.050389 restraints weight = 98718.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052138 restraints weight = 55645.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053384 restraints weight = 37975.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054127 restraints weight = 29366.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054786 restraints weight = 24802.050| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24164 Z= 0.124 Angle : 0.531 8.311 32736 Z= 0.272 Chirality : 0.037 0.184 3732 Planarity : 0.004 0.039 4076 Dihedral : 4.017 43.155 3200 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.33 % Allowed : 14.11 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.68 (0.16), residues: 2880 helix: 2.57 (0.11), residues: 2176 sheet: None (None), residues: 0 loop : -0.87 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 368 TYR 0.009 0.001 TYR C 37 PHE 0.028 0.001 PHE B 568 TRP 0.018 0.001 TRP A 432 HIS 0.002 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24148) covalent geometry : angle 0.53037 / 0.27 (32724) hydrogen bonds : bond 0.03938 / 2.67 ( 1600) hydrogen bonds : angle 3.45282 / 2.51 ( 4740) metal coordination : bond 0.00293 / 0.21 ( 16) metal coordination : angle 0.98450 / 0.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2825.54 seconds wall clock time: 49 minutes 59.63 seconds (2999.63 seconds total)