Starting phenix.real_space_refine on Wed Aug 5 18:46:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrk_73369/08_2026/9yrk_73369.map" } resolution = 3.1 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= 0.005 sd= 1.123 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: 8 Type Number sf(0) Gaussians Zn 10 6.06 5 P 40 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 6820 2.51 5 N 1861 2.21 5 O 2113 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10951 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4086 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 bond proxies already assigned to first conformer: 4182 Chain: "C" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "D" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 Chain: "E" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 726 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 31} Chain breaks: 1 Chain: "F" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'EIF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 50.800 81.848 70.121 1.00 73.48 S ATOM 546 SG CYS A 77 50.191 79.719 73.260 1.00 72.77 S ATOM 651 SG CYS A 90 51.983 83.095 73.589 1.00 88.96 S ATOM 854 SG CYS A 117 54.920 101.867 67.492 1.00111.12 S ATOM 874 SG CYS A 120 51.770 102.970 69.233 1.00107.36 S ATOM 935 SG CYS A 128 51.975 103.120 65.491 1.00111.74 S ATOM 947 SG CYS A 130 53.922 105.645 67.557 1.00131.38 S ATOM 2578 SG CYS B 207 68.647 65.900 48.571 1.00 75.70 S ATOM 2598 SG CYS B 210 70.093 64.366 45.470 1.00 76.68 S ATOM 2719 SG CYS B 226 68.590 62.165 48.181 1.00 69.69 S ATOM 3019 SG CYS B 261 52.158 34.393 55.304 1.00 85.49 S ATOM 3149 SG CYS B 279 51.574 38.043 53.917 1.00 81.92 S ATOM 4539 SG CYS B 452 82.592 28.149 10.706 1.00155.14 S ATOM 4653 SG CYS B 477 82.603 27.090 14.450 1.00148.82 S ATOM 4695 SG CYS B 484 82.639 30.860 13.393 1.00150.07 S ATOM 5561 SG CYS C 74 46.402 26.663 113.678 1.00 75.54 S ATOM 5587 SG CYS C 77 49.697 26.654 111.697 1.00 73.97 S ATOM 5692 SG CYS C 90 48.701 23.563 113.709 1.00 87.05 S ATOM 5895 SG CYS C 117 35.472 11.351 122.173 1.00108.55 S ATOM 5915 SG CYS C 120 34.687 9.978 118.804 1.00105.44 S ATOM 5976 SG CYS C 128 32.074 11.999 120.738 1.00105.74 S ATOM 5988 SG CYS C 130 32.888 8.484 121.861 1.00116.71 S ATOM 7609 SG CYS D 207 47.559 50.600 135.189 1.00 76.66 S ATOM 7629 SG CYS D 210 46.569 53.592 137.331 1.00 96.46 S ATOM 7750 SG CYS D 226 49.326 53.908 134.630 1.00 85.16 S ATOM 8050 SG CYS D 261 62.440 73.444 111.570 1.00 83.87 S ATOM 8180 SG CYS D 279 59.120 71.462 112.245 1.00 82.36 S ATOM 9570 SG CYS D 452 48.341 102.755 153.681 1.00164.65 S ATOM 9684 SG CYS D 477 51.739 101.302 154.476 1.00148.66 S ATOM 9726 SG CYS D 484 48.665 99.090 154.959 1.00153.54 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 95 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS B 95 " occ=0.58 Time building chain proxies: 2.89, per 1000 atoms: 0.26 Number of scatterers: 10951 At special positions: 0 Unit cell: (99.7332, 120.109, 169.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 10 29.99 S 104 16.00 P 40 15.00 Mg 2 11.99 F 1 9.00 O 2113 8.00 N 1861 7.00 C 6820 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 533.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 477 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 77 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 74 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 117 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 128 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 120 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 130 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 229 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 207 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 210 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 226 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" NE2 HIS D 257 " pdb="ZN ZN D 603 " - pdb=" ND1 HIS D 264 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 279 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 261 " pdb=" ZN D 604 " pdb="ZN ZN D 604 " - pdb=" ND1 HIS D 487 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 477 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 452 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 484 " Number of angles added : 33 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2402 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 17 sheets defined 30.1% alpha, 15.5% beta 19 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.237A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.605A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.651A pdb=" N MET B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 158 through 174 removed outlier: 4.122A pdb=" N ILE B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.033A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.606A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.510A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.634A pdb=" N ALA B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.186A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.637A pdb=" N LEU B 519 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP B 520 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 12 through 18 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 74 through 80 Processing helix chain 'C' and resid 85 through 89 removed outlier: 4.293A pdb=" N PHE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 148 through 153 removed outlier: 4.513A pdb=" N LEU D 152 " --> pdb=" O HIS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.824A pdb=" N ILE D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 198 removed outlier: 4.111A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.608A pdb=" N VAL D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 324 Processing helix chain 'D' and resid 432 through 437 removed outlier: 3.607A pdb=" N ALA D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 437 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 Processing helix chain 'D' and resid 484 through 504 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.561A pdb=" N TRP D 520 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN D 521 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.698A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.965A pdb=" N GLU B 364 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 328 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU B 383 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS B 330 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TRP B 385 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE B 332 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.374A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 55 removed outlier: 4.662A pdb=" N TYR D 124 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 118 removed outlier: 5.643A pdb=" N CYS D 94 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 108 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AB6, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.614A pdb=" N VAL D 328 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU D 383 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS D 330 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TRP D 385 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE D 332 " --> pdb=" O TRP D 385 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS D 382 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N CYS D 399 " --> pdb=" O CYS D 382 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE D 384 " --> pdb=" O CYS D 399 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE D 401 " --> pdb=" O PHE D 384 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER D 396 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB8, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.356A pdb=" N TYR D 446 " --> pdb=" O ILE D 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 324 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3060 1.33 - 1.45: 2284 1.45 - 1.57: 5760 1.57 - 1.69: 77 1.69 - 1.81: 136 Bond restraints: 11317 Sorted by residual: bond pdb=" O3 EIF E 101 " pdb=" P EIF E 101 " ideal model delta sigma weight residual 1.670 1.520 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N EIF E 101 " pdb=" C6 EIF E 101 " ideal model delta sigma weight residual 1.440 1.372 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 EIF E 101 " pdb=" P EIF E 101 " ideal model delta sigma weight residual 1.463 1.518 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C7 EIF E 101 " pdb=" C8 EIF E 101 " ideal model delta sigma weight residual 1.430 1.376 0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C10 EIF E 101 " pdb=" N4 EIF E 101 " ideal model delta sigma weight residual 1.444 1.392 0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 11312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 15413 2.54 - 5.08: 144 5.08 - 7.62: 13 7.62 - 10.16: 2 10.16 - 12.69: 1 Bond angle restraints: 15573 Sorted by residual: angle pdb=" O5' G E 3 " pdb=" C5' G E 3 " pdb=" C4' G E 3 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" O3 EIF E 101 " pdb=" P EIF E 101 " pdb=" O4 EIF E 101 " ideal model delta sigma weight residual 128.40 115.71 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N ASN B 478 " pdb=" CA ASN B 478 " pdb=" C ASN B 478 " ideal model delta sigma weight residual 113.72 108.39 5.33 1.30e+00 5.92e-01 1.68e+01 angle pdb=" O5' G E 9 " pdb=" C5' G E 9 " pdb=" C4' G E 9 " ideal model delta sigma weight residual 109.40 112.53 -3.13 8.00e-01 1.56e+00 1.53e+01 angle pdb=" C4' G E 7 " pdb=" C3' G E 7 " pdb=" C2' G E 7 " ideal model delta sigma weight residual 102.60 98.89 3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 15568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6188 17.98 - 35.96: 370 35.96 - 53.94: 82 53.94 - 71.92: 44 71.92 - 89.90: 17 Dihedral angle restraints: 6701 sinusoidal: 2959 harmonic: 3742 Sorted by residual: dihedral pdb=" CA THR D 97 " pdb=" C THR D 97 " pdb=" N ARG D 98 " pdb=" CA ARG D 98 " ideal model delta harmonic sigma weight residual 180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA HIS D 268 " pdb=" C HIS D 268 " pdb=" N VAL D 269 " pdb=" CA VAL D 269 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA CYS B 356 " pdb=" C CYS B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1588 0.090 - 0.180: 148 0.180 - 0.270: 1 0.270 - 0.359: 0 0.359 - 0.449: 3 Chirality restraints: 1740 Sorted by residual: chirality pdb=" P C E 6 " pdb=" OP1 C E 6 " pdb=" OP2 C E 6 " pdb=" O5' C E 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" P G E 7 " pdb=" OP1 G E 7 " pdb=" OP2 G E 7 " pdb=" O5' G E 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C2 EIF E 101 " pdb=" O EIF E 101 " pdb=" C1 EIF E 101 " pdb=" C3 EIF E 101 " both_signs ideal model delta sigma weight residual False -2.89 -2.50 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 1737 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 19 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO D 20 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 19 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO B 20 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 20 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 20 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 127 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO D 128 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.024 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 145 2.66 - 3.22: 9473 3.22 - 3.78: 16990 3.78 - 4.34: 24148 4.34 - 4.90: 38852 Nonbonded interactions: 89608 Sorted by model distance: nonbonded pdb=" OP1 C F 6 " pdb="MG MG D 601 " model vdw 2.094 2.170 nonbonded pdb=" O LEU D 519 " pdb=" OG1 THR D 522 " model vdw 2.284 3.040 nonbonded pdb=" O TYR D 370 " pdb=" OG SER D 374 " model vdw 2.310 3.040 nonbonded pdb=" OD2 ASP D 90 " pdb="MG MG D 601 " model vdw 2.325 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.327 2.170 ... (remaining 89603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 3 through 94 or resid 96 through 604)) selection = (chain 'D' and (resid 3 through 94 or resid 96 through 604)) } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.190 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.004 0.150 11358 Z= 0.210 Angle : 0.633 12.695 15606 Z= 0.387 Chirality : 0.050 0.449 1740 Planarity : 0.005 0.050 1846 Dihedral : 14.033 89.900 4299 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: -0.33 (0.23), residues: 1275 helix: 0.12 (0.30), residues: 292 sheet: -1.06 (0.38), residues: 173 loop : -0.05 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.019 0.001 TYR B 420 PHE 0.018 0.001 PHE B 133 TRP 0.013 0.001 TRP B 227 HIS 0.005 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (11317) covalent geometry : angle 0.62721 / 0.39 (15573) hydrogen bonds : bond 0.14426 / 9.33 ( 362) hydrogen bonds : angle 5.95311 / 4.01 ( 962) metal coordination : bond 0.00752 / 0.49 ( 40) metal coordination : angle 1.94476 / 1.37 ( 33) Misc. bond : bond 0.04112 / 2.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.7852 (m) cc_final: 0.7453 (m) REVERT: A 56 THR cc_start: 0.8267 (p) cc_final: 0.8058 (p) REVERT: A 58 THR cc_start: 0.8458 (t) cc_final: 0.8084 (t) REVERT: B 13 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7742 (mtmt) REVERT: B 71 ASN cc_start: 0.7844 (m110) cc_final: 0.7574 (t0) REVERT: B 92 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 98 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7792 (mtm110) REVERT: B 122 THR cc_start: 0.8316 (m) cc_final: 0.8042 (p) REVERT: B 139 LYS cc_start: 0.8073 (tttt) cc_final: 0.7848 (ptmm) REVERT: B 154 TYR cc_start: 0.8210 (m-80) cc_final: 0.7920 (m-80) REVERT: B 212 ARG cc_start: 0.8313 (mtt90) cc_final: 0.8099 (mtt-85) REVERT: B 284 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8134 (mm-30) REVERT: B 304 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7912 (mmtt) REVERT: B 318 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7919 (ttpp) REVERT: B 324 ASP cc_start: 0.6959 (m-30) cc_final: 0.6387 (m-30) REVERT: B 325 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7631 (mtmm) REVERT: B 347 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 349 LYS cc_start: 0.8227 (mttt) cc_final: 0.7884 (mttt) REVERT: B 352 ASP cc_start: 0.6682 (t0) cc_final: 0.6037 (t0) REVERT: B 398 VAL cc_start: 0.8520 (t) cc_final: 0.8250 (p) REVERT: B 404 ARG cc_start: 0.7591 (mtm180) cc_final: 0.7277 (mtm180) REVERT: B 421 VAL cc_start: 0.7829 (t) cc_final: 0.7568 (t) REVERT: B 491 TYR cc_start: 0.7647 (t80) cc_final: 0.7339 (t80) REVERT: B 492 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7487 (mtm110) REVERT: B 500 MET cc_start: 0.7616 (tpp) cc_final: 0.6983 (tpp) REVERT: C 51 THR cc_start: 0.8679 (t) cc_final: 0.8424 (p) REVERT: C 56 THR cc_start: 0.8382 (p) cc_final: 0.8094 (p) REVERT: C 58 THR cc_start: 0.7612 (t) cc_final: 0.7302 (m) REVERT: D 14 VAL cc_start: 0.8618 (m) cc_final: 0.8252 (m) REVERT: D 30 ASP cc_start: 0.7769 (t70) cc_final: 0.7415 (t0) REVERT: D 40 VAL cc_start: 0.8322 (p) cc_final: 0.8118 (t) REVERT: D 61 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7494 (mtpt) REVERT: D 135 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7162 (mtt180) REVERT: D 211 ASP cc_start: 0.7895 (t0) cc_final: 0.7530 (t0) REVERT: D 231 ILE cc_start: 0.8520 (mm) cc_final: 0.8240 (tt) REVERT: D 246 GLN cc_start: 0.8165 (mt0) cc_final: 0.7923 (mt0) REVERT: D 259 LEU cc_start: 0.8576 (mt) cc_final: 0.8287 (mp) REVERT: D 263 VAL cc_start: 0.8618 (t) cc_final: 0.8349 (p) REVERT: D 295 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8392 (mt-10) REVERT: D 310 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7748 (mtp180) REVERT: D 311 LYS cc_start: 0.8431 (tttt) cc_final: 0.8180 (ttmm) REVERT: D 318 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7876 (ttpt) REVERT: D 324 ASP cc_start: 0.7790 (m-30) cc_final: 0.7242 (m-30) REVERT: D 326 PHE cc_start: 0.8324 (m-80) cc_final: 0.7971 (m-10) REVERT: D 339 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7885 (mtpt) REVERT: D 351 TYR cc_start: 0.7783 (m-80) cc_final: 0.7319 (m-80) REVERT: D 423 LYS cc_start: 0.8297 (mttm) cc_final: 0.7994 (mtpp) REVERT: D 447 TYR cc_start: 0.7883 (t80) cc_final: 0.7681 (t80) REVERT: D 491 TYR cc_start: 0.7969 (t80) cc_final: 0.7734 (t80) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1231 time to fit residues: 47.1798 Evaluate side-chains 246 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN B 313 GLN B 354 GLN C 3 ASN C 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102279 restraints weight = 21800.356| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3126 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11358 Z= 0.153 Angle : 0.505 5.362 15606 Z= 0.269 Chirality : 0.042 0.159 1740 Planarity : 0.005 0.051 1846 Dihedral : 11.960 74.456 2013 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.90 % Allowed : 10.77 % Favored : 88.33 % 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: -0.09 (0.24), residues: 1275 helix: 0.57 (0.31), residues: 296 sheet: -1.12 (0.36), residues: 173 loop : 0.05 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 391 TYR 0.017 0.001 TYR B 420 PHE 0.036 0.002 PHE B 350 TRP 0.016 0.001 TRP B 348 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11317) covalent geometry : angle 0.49612 / 0.27 (15573) hydrogen bonds : bond 0.04683 / 3.13 ( 362) hydrogen bonds : angle 4.52311 / 3.11 ( 962) metal coordination : bond 0.00919 / 0.63 ( 40) metal coordination : angle 2.15410 / 1.40 ( 33) Misc. bond : bond 0.00162 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7540 (tp30) REVERT: A 56 THR cc_start: 0.8331 (p) cc_final: 0.8100 (p) REVERT: A 58 THR cc_start: 0.8477 (t) cc_final: 0.8110 (t) REVERT: A 122 MET cc_start: 0.8580 (mmt) cc_final: 0.8105 (mmm) REVERT: B 13 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7775 (mtmt) REVERT: B 71 ASN cc_start: 0.7826 (m110) cc_final: 0.7620 (t0) REVERT: B 77 GLU cc_start: 0.7395 (mp0) cc_final: 0.7161 (mp0) REVERT: B 98 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7833 (mtm110) REVERT: B 122 THR cc_start: 0.8329 (m) cc_final: 0.8021 (p) REVERT: B 139 LYS cc_start: 0.8154 (tttt) cc_final: 0.7888 (ptmm) REVERT: B 153 MET cc_start: 0.8489 (mmm) cc_final: 0.8215 (mmm) REVERT: B 154 TYR cc_start: 0.8187 (m-80) cc_final: 0.7833 (m-80) REVERT: B 195 MET cc_start: 0.8281 (mtt) cc_final: 0.8030 (mtt) REVERT: B 212 ARG cc_start: 0.8302 (mtt90) cc_final: 0.8089 (mtt-85) REVERT: B 284 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 304 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7904 (mmtt) REVERT: B 315 MET cc_start: 0.8364 (tpp) cc_final: 0.8121 (tpp) REVERT: B 318 LYS cc_start: 0.8220 (ttpt) cc_final: 0.8018 (ttpp) REVERT: B 324 ASP cc_start: 0.7145 (m-30) cc_final: 0.6601 (m-30) REVERT: B 325 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7545 (mtmm) REVERT: B 347 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 349 LYS cc_start: 0.8268 (mttt) cc_final: 0.7746 (mttt) REVERT: B 352 ASP cc_start: 0.6810 (t0) cc_final: 0.6088 (t0) REVERT: B 398 VAL cc_start: 0.8533 (t) cc_final: 0.8274 (p) REVERT: B 404 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7184 (mtm180) REVERT: B 421 VAL cc_start: 0.7794 (t) cc_final: 0.7530 (t) REVERT: B 491 TYR cc_start: 0.7629 (t80) cc_final: 0.7323 (t80) REVERT: B 492 ARG cc_start: 0.7817 (mtm180) cc_final: 0.7479 (mtm110) REVERT: C 51 THR cc_start: 0.8626 (t) cc_final: 0.8379 (p) REVERT: C 56 THR cc_start: 0.8381 (p) cc_final: 0.8109 (p) REVERT: D 61 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7453 (mtpt) REVERT: D 169 MET cc_start: 0.8421 (ttp) cc_final: 0.8179 (tmm) REVERT: D 211 ASP cc_start: 0.7841 (t0) cc_final: 0.7465 (t0) REVERT: D 231 ILE cc_start: 0.8560 (mm) cc_final: 0.8295 (tt) REVERT: D 246 GLN cc_start: 0.8170 (mt0) cc_final: 0.7837 (mt0) REVERT: D 259 LEU cc_start: 0.8594 (mt) cc_final: 0.8326 (mp) REVERT: D 263 VAL cc_start: 0.8599 (t) cc_final: 0.8316 (p) REVERT: D 295 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8110 (mt-10) REVERT: D 310 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7688 (mtp180) REVERT: D 311 LYS cc_start: 0.8396 (tttt) cc_final: 0.8150 (ttmm) REVERT: D 318 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7870 (ttpt) REVERT: D 324 ASP cc_start: 0.7838 (m-30) cc_final: 0.7229 (m-30) REVERT: D 326 PHE cc_start: 0.8295 (m-80) cc_final: 0.7790 (m-10) REVERT: D 331 ASP cc_start: 0.7643 (t0) cc_final: 0.7165 (t0) REVERT: D 423 LYS cc_start: 0.8405 (mttm) cc_final: 0.8136 (mtpp) REVERT: D 491 TYR cc_start: 0.7967 (t80) cc_final: 0.7716 (t80) outliers start: 10 outliers final: 4 residues processed: 256 average time/residue: 0.1191 time to fit residues: 41.1020 Evaluate side-chains 248 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 309 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.0020 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 HIS C 40 ASN C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102190 restraints weight = 24710.615| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.44 r_work: 0.3119 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11358 Z= 0.126 Angle : 0.486 7.539 15606 Z= 0.255 Chirality : 0.041 0.157 1740 Planarity : 0.004 0.043 1846 Dihedral : 11.889 74.113 2013 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.81 % Allowed : 11.86 % Favored : 87.33 % 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: 0.08 (0.24), residues: 1275 helix: 0.83 (0.32), residues: 294 sheet: -1.01 (0.37), residues: 173 loop : 0.10 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.015 0.001 TYR D 351 PHE 0.021 0.001 PHE D 444 TRP 0.021 0.001 TRP B 348 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11317) covalent geometry : angle 0.47802 / 0.25 (15573) hydrogen bonds : bond 0.04146 / 2.76 ( 362) hydrogen bonds : angle 4.28405 / 2.95 ( 962) metal coordination : bond 0.00725 / 0.52 ( 40) metal coordination : angle 1.98796 / 1.32 ( 33) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 0.380 Fit side-chains REVERT: A 6 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7605 (tp30) REVERT: A 58 THR cc_start: 0.8450 (t) cc_final: 0.8077 (t) REVERT: B 13 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7755 (mtmt) REVERT: B 71 ASN cc_start: 0.7821 (m110) cc_final: 0.7583 (t0) REVERT: B 77 GLU cc_start: 0.7421 (mp0) cc_final: 0.7171 (mp0) REVERT: B 98 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7889 (mtm110) REVERT: B 122 THR cc_start: 0.8375 (m) cc_final: 0.8037 (p) REVERT: B 139 LYS cc_start: 0.8150 (tttt) cc_final: 0.7872 (ptmm) REVERT: B 153 MET cc_start: 0.8484 (mmm) cc_final: 0.8251 (mmm) REVERT: B 154 TYR cc_start: 0.8198 (m-80) cc_final: 0.7806 (m-80) REVERT: B 212 ARG cc_start: 0.8301 (mtt90) cc_final: 0.8082 (mtt-85) REVERT: B 284 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8158 (mm-30) REVERT: B 304 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7933 (mmtt) REVERT: B 315 MET cc_start: 0.8389 (tpp) cc_final: 0.8159 (tpp) REVERT: B 324 ASP cc_start: 0.7162 (m-30) cc_final: 0.6659 (m-30) REVERT: B 339 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7330 (mtmm) REVERT: B 347 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 349 LYS cc_start: 0.8333 (mttt) cc_final: 0.7696 (mttt) REVERT: B 351 TYR cc_start: 0.8507 (m-80) cc_final: 0.7960 (m-80) REVERT: B 352 ASP cc_start: 0.6864 (t0) cc_final: 0.6135 (t0) REVERT: B 398 VAL cc_start: 0.8539 (t) cc_final: 0.8291 (p) REVERT: B 404 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7235 (mtm180) REVERT: B 421 VAL cc_start: 0.7803 (t) cc_final: 0.7549 (t) REVERT: B 491 TYR cc_start: 0.7652 (t80) cc_final: 0.7316 (t80) REVERT: B 492 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7475 (mtm110) REVERT: C 6 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7718 (mm-30) REVERT: C 51 THR cc_start: 0.8636 (t) cc_final: 0.8387 (p) REVERT: C 56 THR cc_start: 0.8361 (p) cc_final: 0.8083 (p) REVERT: D 35 THR cc_start: 0.7548 (m) cc_final: 0.7033 (p) REVERT: D 61 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7461 (mtpt) REVERT: D 211 ASP cc_start: 0.7878 (t0) cc_final: 0.7576 (t0) REVERT: D 231 ILE cc_start: 0.8569 (mm) cc_final: 0.8304 (tt) REVERT: D 246 GLN cc_start: 0.8186 (mt0) cc_final: 0.7868 (mt0) REVERT: D 259 LEU cc_start: 0.8574 (mt) cc_final: 0.8321 (mp) REVERT: D 263 VAL cc_start: 0.8607 (t) cc_final: 0.8317 (p) REVERT: D 295 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 311 LYS cc_start: 0.8402 (tttt) cc_final: 0.8150 (ttmm) REVERT: D 318 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7892 (ttpt) REVERT: D 324 ASP cc_start: 0.7898 (m-30) cc_final: 0.6910 (m-30) REVERT: D 326 PHE cc_start: 0.8204 (m-80) cc_final: 0.7988 (m-10) REVERT: D 423 LYS cc_start: 0.8426 (mttm) cc_final: 0.8106 (mtpp) REVERT: D 491 TYR cc_start: 0.7980 (t80) cc_final: 0.7642 (t80) REVERT: D 511 TYR cc_start: 0.8061 (p90) cc_final: 0.7242 (p90) outliers start: 9 outliers final: 6 residues processed: 254 average time/residue: 0.1337 time to fit residues: 45.1693 Evaluate side-chains 240 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 309 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 HIS C 40 ASN C 98 GLN D 108 GLN D 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101636 restraints weight = 26100.763| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.53 r_work: 0.3107 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11358 Z= 0.146 Angle : 0.485 6.900 15606 Z= 0.255 Chirality : 0.041 0.153 1740 Planarity : 0.004 0.044 1846 Dihedral : 11.873 74.089 2013 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.45 % Allowed : 12.04 % Favored : 86.52 % 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: 0.08 (0.24), residues: 1275 helix: 0.87 (0.31), residues: 294 sheet: -1.12 (0.35), residues: 185 loop : 0.14 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.018 0.001 TYR D 447 PHE 0.021 0.002 PHE D 444 TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11317) covalent geometry : angle 0.47767 / 0.25 (15573) hydrogen bonds : bond 0.04076 / 2.71 ( 362) hydrogen bonds : angle 4.22571 / 2.91 ( 962) metal coordination : bond 0.00770 / 0.55 ( 40) metal coordination : angle 1.94417 / 1.30 ( 33) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7664 (tp30) REVERT: B 65 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7487 (tm-30) REVERT: B 71 ASN cc_start: 0.7819 (m110) cc_final: 0.7598 (t0) REVERT: B 77 GLU cc_start: 0.7474 (mp0) cc_final: 0.7227 (mp0) REVERT: B 139 LYS cc_start: 0.8179 (tttt) cc_final: 0.7912 (ptmm) REVERT: B 153 MET cc_start: 0.8475 (mmm) cc_final: 0.8031 (mmm) REVERT: B 154 TYR cc_start: 0.8201 (m-80) cc_final: 0.7818 (m-80) REVERT: B 212 ARG cc_start: 0.8310 (mtt90) cc_final: 0.8090 (mtt-85) REVERT: B 284 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 295 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 304 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7940 (mmtt) REVERT: B 315 MET cc_start: 0.8415 (tpp) cc_final: 0.8190 (tpp) REVERT: B 324 ASP cc_start: 0.7175 (m-30) cc_final: 0.6681 (m-30) REVERT: B 339 LYS cc_start: 0.7633 (mtmm) cc_final: 0.7337 (mtmm) REVERT: B 347 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7228 (mm-30) REVERT: B 349 LYS cc_start: 0.8378 (mttt) cc_final: 0.7870 (mttt) REVERT: B 352 ASP cc_start: 0.6869 (t0) cc_final: 0.6141 (t0) REVERT: B 398 VAL cc_start: 0.8570 (t) cc_final: 0.8324 (p) REVERT: B 404 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7231 (mtm180) REVERT: B 421 VAL cc_start: 0.7853 (t) cc_final: 0.7591 (t) REVERT: B 491 TYR cc_start: 0.7715 (t80) cc_final: 0.7347 (t80) REVERT: B 492 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7480 (mtm110) REVERT: B 495 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8285 (tp) REVERT: C 6 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 51 THR cc_start: 0.8652 (t) cc_final: 0.8396 (p) REVERT: C 56 THR cc_start: 0.8345 (p) cc_final: 0.8070 (p) REVERT: D 35 THR cc_start: 0.7577 (m) cc_final: 0.7068 (p) REVERT: D 61 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7482 (mtpt) REVERT: D 169 MET cc_start: 0.8505 (ttp) cc_final: 0.8230 (tmm) REVERT: D 211 ASP cc_start: 0.7882 (t0) cc_final: 0.7458 (t0) REVERT: D 231 ILE cc_start: 0.8579 (mm) cc_final: 0.8306 (tt) REVERT: D 246 GLN cc_start: 0.8189 (mt0) cc_final: 0.7892 (mt0) REVERT: D 259 LEU cc_start: 0.8605 (mt) cc_final: 0.8359 (mp) REVERT: D 263 VAL cc_start: 0.8614 (t) cc_final: 0.8327 (p) REVERT: D 295 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8327 (mt-10) REVERT: D 311 LYS cc_start: 0.8418 (tttt) cc_final: 0.8190 (ttmm) REVERT: D 318 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7933 (ttpt) REVERT: D 324 ASP cc_start: 0.7854 (m-30) cc_final: 0.7231 (m-30) REVERT: D 326 PHE cc_start: 0.8246 (m-80) cc_final: 0.8017 (m-10) REVERT: D 352 ASP cc_start: 0.7011 (m-30) cc_final: 0.6753 (m-30) REVERT: D 395 ASN cc_start: 0.7403 (p0) cc_final: 0.6920 (p0) REVERT: D 491 TYR cc_start: 0.8011 (t80) cc_final: 0.7696 (t80) outliers start: 16 outliers final: 10 residues processed: 248 average time/residue: 0.1273 time to fit residues: 42.4466 Evaluate side-chains 247 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 78 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 160 ASN B 254 GLN B 314 HIS C 40 ASN C 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102650 restraints weight = 23689.729| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.37 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11358 Z= 0.115 Angle : 0.470 9.715 15606 Z= 0.246 Chirality : 0.041 0.184 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.828 73.995 2013 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 13.12 % Favored : 85.70 % 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: 0.17 (0.24), residues: 1275 helix: 1.01 (0.31), residues: 294 sheet: -1.08 (0.35), residues: 185 loop : 0.18 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.018 0.001 TYR D 447 PHE 0.025 0.001 PHE D 444 TRP 0.008 0.001 TRP B 385 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (11317) covalent geometry : angle 0.46285 / 0.25 (15573) hydrogen bonds : bond 0.03742 / 2.51 ( 362) hydrogen bonds : angle 4.08939 / 2.82 ( 962) metal coordination : bond 0.00614 / 0.43 ( 40) metal coordination : angle 1.82198 / 1.22 ( 33) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8011 (m) cc_final: 0.7567 (m) REVERT: A 6 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7650 (tp30) REVERT: B 65 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7465 (tm-30) REVERT: B 77 GLU cc_start: 0.7375 (mp0) cc_final: 0.7124 (mp0) REVERT: B 139 LYS cc_start: 0.8132 (tttt) cc_final: 0.7848 (ptmm) REVERT: B 153 MET cc_start: 0.8451 (mmm) cc_final: 0.8018 (mmm) REVERT: B 154 TYR cc_start: 0.8129 (m-80) cc_final: 0.7756 (m-80) REVERT: B 212 ARG cc_start: 0.8265 (mtt90) cc_final: 0.8036 (mtt-85) REVERT: B 295 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 315 MET cc_start: 0.8423 (tpp) cc_final: 0.8183 (tpp) REVERT: B 324 ASP cc_start: 0.7113 (m-30) cc_final: 0.6669 (m-30) REVERT: B 325 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7451 (mmmm) REVERT: B 339 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7353 (mtmm) REVERT: B 347 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 349 LYS cc_start: 0.8298 (mttt) cc_final: 0.7790 (mttt) REVERT: B 352 ASP cc_start: 0.6806 (t0) cc_final: 0.6087 (t0) REVERT: B 398 VAL cc_start: 0.8559 (t) cc_final: 0.8302 (p) REVERT: B 404 ARG cc_start: 0.7446 (mtm180) cc_final: 0.7057 (mtm180) REVERT: B 421 VAL cc_start: 0.7797 (t) cc_final: 0.7540 (t) REVERT: B 491 TYR cc_start: 0.7640 (t80) cc_final: 0.7344 (t80) REVERT: B 492 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7416 (mtm110) REVERT: C 6 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 51 THR cc_start: 0.8643 (t) cc_final: 0.8376 (p) REVERT: C 56 THR cc_start: 0.8333 (p) cc_final: 0.8040 (p) REVERT: C 101 THR cc_start: 0.8183 (t) cc_final: 0.7949 (m) REVERT: D 35 THR cc_start: 0.7541 (m) cc_final: 0.7034 (p) REVERT: D 61 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7429 (mtpt) REVERT: D 169 MET cc_start: 0.8461 (ttp) cc_final: 0.8180 (tmm) REVERT: D 211 ASP cc_start: 0.7852 (t0) cc_final: 0.7492 (t0) REVERT: D 231 ILE cc_start: 0.8566 (mm) cc_final: 0.8286 (tt) REVERT: D 246 GLN cc_start: 0.8161 (mt0) cc_final: 0.7906 (mt0) REVERT: D 259 LEU cc_start: 0.8558 (mt) cc_final: 0.8316 (mp) REVERT: D 263 VAL cc_start: 0.8583 (t) cc_final: 0.8305 (p) REVERT: D 295 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8283 (mt-10) REVERT: D 311 LYS cc_start: 0.8395 (tttt) cc_final: 0.8147 (ttmm) REVERT: D 318 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7843 (ttpt) REVERT: D 324 ASP cc_start: 0.7831 (m-30) cc_final: 0.6961 (m-30) REVERT: D 395 ASN cc_start: 0.7376 (p0) cc_final: 0.6882 (p0) REVERT: D 491 TYR cc_start: 0.7956 (t80) cc_final: 0.7597 (t80) REVERT: D 511 TYR cc_start: 0.8067 (p90) cc_final: 0.7293 (p90) outliers start: 13 outliers final: 9 residues processed: 249 average time/residue: 0.1296 time to fit residues: 43.5561 Evaluate side-chains 246 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 237 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 314 HIS C 40 ASN C 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101660 restraints weight = 25995.094| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.47 r_work: 0.3111 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11358 Z= 0.149 Angle : 0.489 9.893 15606 Z= 0.255 Chirality : 0.042 0.148 1740 Planarity : 0.004 0.043 1846 Dihedral : 11.817 74.107 2013 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.18 % Allowed : 13.85 % Favored : 84.98 % 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: 0.17 (0.24), residues: 1275 helix: 1.03 (0.31), residues: 294 sheet: -1.04 (0.34), residues: 195 loop : 0.18 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.019 0.001 TYR D 447 PHE 0.032 0.002 PHE D 326 TRP 0.009 0.001 TRP B 520 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11317) covalent geometry : angle 0.48188 / 0.25 (15573) hydrogen bonds : bond 0.03899 / 2.61 ( 362) hydrogen bonds : angle 4.13992 / 2.86 ( 962) metal coordination : bond 0.00762 / 0.53 ( 40) metal coordination : angle 1.87436 / 1.25 ( 33) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8048 (m) cc_final: 0.7586 (m) REVERT: A 6 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7703 (tp30) REVERT: B 65 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7452 (tm-30) REVERT: B 77 GLU cc_start: 0.7446 (mp0) cc_final: 0.7197 (mp0) REVERT: B 139 LYS cc_start: 0.8171 (tttt) cc_final: 0.7883 (ptmm) REVERT: B 153 MET cc_start: 0.8424 (mmm) cc_final: 0.8025 (mmm) REVERT: B 154 TYR cc_start: 0.8144 (m-80) cc_final: 0.7784 (m-80) REVERT: B 212 ARG cc_start: 0.8284 (mtt90) cc_final: 0.8056 (mtt-85) REVERT: B 295 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 304 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7899 (mmtt) REVERT: B 315 MET cc_start: 0.8425 (tpp) cc_final: 0.8193 (tpp) REVERT: B 324 ASP cc_start: 0.7137 (m-30) cc_final: 0.6693 (m-30) REVERT: B 325 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7640 (mmtm) REVERT: B 339 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7384 (mtmm) REVERT: B 347 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 349 LYS cc_start: 0.8378 (mttt) cc_final: 0.7855 (mttt) REVERT: B 352 ASP cc_start: 0.6867 (t0) cc_final: 0.6115 (t0) REVERT: B 398 VAL cc_start: 0.8535 (t) cc_final: 0.8279 (p) REVERT: B 404 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7232 (mtm180) REVERT: B 421 VAL cc_start: 0.7849 (t) cc_final: 0.7593 (t) REVERT: B 491 TYR cc_start: 0.7687 (t80) cc_final: 0.7368 (t80) REVERT: B 492 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7448 (mtm110) REVERT: C 51 THR cc_start: 0.8678 (t) cc_final: 0.8391 (p) REVERT: C 56 THR cc_start: 0.8331 (p) cc_final: 0.8039 (p) REVERT: C 101 THR cc_start: 0.8201 (t) cc_final: 0.7972 (m) REVERT: D 35 THR cc_start: 0.7551 (m) cc_final: 0.7073 (p) REVERT: D 61 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7462 (mtpt) REVERT: D 169 MET cc_start: 0.8484 (ttp) cc_final: 0.8209 (tmm) REVERT: D 211 ASP cc_start: 0.7877 (t0) cc_final: 0.7514 (t0) REVERT: D 231 ILE cc_start: 0.8564 (mm) cc_final: 0.8289 (tt) REVERT: D 246 GLN cc_start: 0.8171 (mt0) cc_final: 0.7930 (mt0) REVERT: D 259 LEU cc_start: 0.8562 (mt) cc_final: 0.8334 (mp) REVERT: D 263 VAL cc_start: 0.8582 (t) cc_final: 0.8308 (p) REVERT: D 295 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 310 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7755 (mtp180) REVERT: D 311 LYS cc_start: 0.8463 (tttt) cc_final: 0.8220 (ttmm) REVERT: D 318 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7864 (ttpt) REVERT: D 324 ASP cc_start: 0.7859 (m-30) cc_final: 0.7295 (m-30) REVERT: D 395 ASN cc_start: 0.7353 (p0) cc_final: 0.6818 (p0) REVERT: D 491 TYR cc_start: 0.7983 (t80) cc_final: 0.7621 (t80) REVERT: D 511 TYR cc_start: 0.8084 (p90) cc_final: 0.7401 (p90) REVERT: D 514 PHE cc_start: 0.7909 (t80) cc_final: 0.7689 (t80) outliers start: 13 outliers final: 10 residues processed: 245 average time/residue: 0.1289 time to fit residues: 42.7940 Evaluate side-chains 245 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 0.0470 chunk 42 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 overall best weight: 0.1886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 254 GLN B 314 HIS C 40 ASN C 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103215 restraints weight = 24936.728| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.43 r_work: 0.3137 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11358 Z= 0.093 Angle : 0.478 12.813 15606 Z= 0.246 Chirality : 0.040 0.152 1740 Planarity : 0.004 0.041 1846 Dihedral : 11.771 74.021 2013 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.00 % Allowed : 14.30 % Favored : 84.71 % 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: 0.22 (0.24), residues: 1275 helix: 1.14 (0.31), residues: 294 sheet: -1.04 (0.36), residues: 173 loop : 0.15 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.021 0.001 TYR D 447 PHE 0.030 0.001 PHE D 444 TRP 0.008 0.001 TRP B 385 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (11317) covalent geometry : angle 0.47207 / 0.25 (15573) hydrogen bonds : bond 0.03458 / 2.33 ( 362) hydrogen bonds : angle 3.97657 / 2.74 ( 962) metal coordination : bond 0.00442 / 0.29 ( 40) metal coordination : angle 1.68249 / 1.13 ( 33) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.395 Fit side-chains REVERT: A 5 THR cc_start: 0.8013 (m) cc_final: 0.7558 (m) REVERT: A 6 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7706 (tp30) REVERT: B 65 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7490 (tm-30) REVERT: B 77 GLU cc_start: 0.7352 (mp0) cc_final: 0.7106 (mp0) REVERT: B 139 LYS cc_start: 0.8179 (tttt) cc_final: 0.7876 (ptmm) REVERT: B 153 MET cc_start: 0.8435 (mmm) cc_final: 0.8022 (mmm) REVERT: B 154 TYR cc_start: 0.8120 (m-80) cc_final: 0.7794 (m-80) REVERT: B 206 THR cc_start: 0.8381 (m) cc_final: 0.8156 (t) REVERT: B 212 ARG cc_start: 0.8254 (mtt90) cc_final: 0.8017 (mtt-85) REVERT: B 315 MET cc_start: 0.8439 (tpp) cc_final: 0.8184 (tpp) REVERT: B 324 ASP cc_start: 0.7099 (m-30) cc_final: 0.6671 (m-30) REVERT: B 325 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7521 (mmmm) REVERT: B 339 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7404 (mtmm) REVERT: B 347 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 349 LYS cc_start: 0.8334 (mttt) cc_final: 0.7725 (mttt) REVERT: B 351 TYR cc_start: 0.8514 (m-80) cc_final: 0.7878 (m-80) REVERT: B 352 ASP cc_start: 0.6844 (t0) cc_final: 0.6086 (t0) REVERT: B 398 VAL cc_start: 0.8538 (t) cc_final: 0.8281 (p) REVERT: B 404 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7097 (mtm180) REVERT: B 421 VAL cc_start: 0.7810 (t) cc_final: 0.7565 (t) REVERT: B 491 TYR cc_start: 0.7630 (t80) cc_final: 0.7319 (t80) REVERT: B 492 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7412 (mtm110) REVERT: C 51 THR cc_start: 0.8636 (t) cc_final: 0.8377 (p) REVERT: C 56 THR cc_start: 0.8289 (p) cc_final: 0.7993 (p) REVERT: C 101 THR cc_start: 0.8174 (t) cc_final: 0.7950 (m) REVERT: D 35 THR cc_start: 0.7549 (m) cc_final: 0.7087 (p) REVERT: D 61 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7421 (mtpt) REVERT: D 169 MET cc_start: 0.8462 (ttp) cc_final: 0.8196 (tmm) REVERT: D 231 ILE cc_start: 0.8549 (mm) cc_final: 0.8264 (tt) REVERT: D 246 GLN cc_start: 0.8151 (mt0) cc_final: 0.7917 (mt0) REVERT: D 259 LEU cc_start: 0.8544 (mt) cc_final: 0.8316 (mp) REVERT: D 263 VAL cc_start: 0.8577 (t) cc_final: 0.8306 (p) REVERT: D 295 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8306 (mt-10) REVERT: D 311 LYS cc_start: 0.8348 (tttt) cc_final: 0.7783 (ttmm) REVERT: D 318 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7822 (ttpt) REVERT: D 324 ASP cc_start: 0.7797 (m-30) cc_final: 0.7264 (m-30) REVERT: D 395 ASN cc_start: 0.7332 (p0) cc_final: 0.6633 (p0) REVERT: D 423 LYS cc_start: 0.8425 (mttm) cc_final: 0.8099 (mtpp) REVERT: D 491 TYR cc_start: 0.7973 (t80) cc_final: 0.7646 (t80) REVERT: D 511 TYR cc_start: 0.8162 (p90) cc_final: 0.7535 (p90) outliers start: 11 outliers final: 9 residues processed: 244 average time/residue: 0.1183 time to fit residues: 39.6520 Evaluate side-chains 242 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 233 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 477 CYS Chi-restraints excluded: chain D residue 495 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.0030 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 52 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 314 HIS C 40 ASN C 98 GLN D 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104842 restraints weight = 21077.782| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.21 r_work: 0.3171 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11358 Z= 0.085 Angle : 0.459 11.712 15606 Z= 0.238 Chirality : 0.040 0.147 1740 Planarity : 0.004 0.039 1846 Dihedral : 11.721 73.996 2013 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.90 % Allowed : 14.75 % Favored : 84.34 % 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: 0.27 (0.24), residues: 1275 helix: 1.24 (0.31), residues: 294 sheet: -1.07 (0.35), residues: 173 loop : 0.17 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.021 0.001 TYR D 447 PHE 0.018 0.001 PHE D 326 TRP 0.007 0.001 TRP B 227 HIS 0.004 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.08 (11317) covalent geometry : angle 0.45342 / 0.24 (15573) hydrogen bonds : bond 0.03255 / 2.20 ( 362) hydrogen bonds : angle 3.88118 / 2.67 ( 962) metal coordination : bond 0.00382 / 0.25 ( 40) metal coordination : angle 1.56374 / 1.06 ( 33) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.371 Fit side-chains REVERT: A 5 THR cc_start: 0.7972 (m) cc_final: 0.7534 (m) REVERT: A 6 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7654 (tp30) REVERT: B 65 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7396 (tm-30) REVERT: B 77 GLU cc_start: 0.7263 (mp0) cc_final: 0.7006 (mp0) REVERT: B 139 LYS cc_start: 0.8155 (tttt) cc_final: 0.7872 (ptmm) REVERT: B 153 MET cc_start: 0.8395 (mmm) cc_final: 0.8004 (mmm) REVERT: B 154 TYR cc_start: 0.8074 (m-80) cc_final: 0.7768 (m-80) REVERT: B 212 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7979 (mtt-85) REVERT: B 295 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8232 (mt-10) REVERT: B 310 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8061 (mtp180) REVERT: B 315 MET cc_start: 0.8420 (tpp) cc_final: 0.8176 (tpp) REVERT: B 324 ASP cc_start: 0.7077 (m-30) cc_final: 0.6668 (m-30) REVERT: B 325 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7566 (mmmm) REVERT: B 339 LYS cc_start: 0.7581 (mtmm) cc_final: 0.7352 (mtmm) REVERT: B 347 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 349 LYS cc_start: 0.8321 (mttt) cc_final: 0.7718 (mttt) REVERT: B 351 TYR cc_start: 0.8494 (m-80) cc_final: 0.7891 (m-80) REVERT: B 352 ASP cc_start: 0.6810 (t0) cc_final: 0.6072 (t0) REVERT: B 398 VAL cc_start: 0.8484 (t) cc_final: 0.8235 (m) REVERT: B 421 VAL cc_start: 0.7786 (t) cc_final: 0.7551 (t) REVERT: B 491 TYR cc_start: 0.7558 (t80) cc_final: 0.7314 (t80) REVERT: B 492 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7378 (mtm110) REVERT: C 51 THR cc_start: 0.8609 (t) cc_final: 0.8365 (p) REVERT: C 56 THR cc_start: 0.8262 (p) cc_final: 0.7959 (p) REVERT: D 35 THR cc_start: 0.7564 (m) cc_final: 0.7135 (p) REVERT: D 61 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7401 (mtpt) REVERT: D 147 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7971 (mtpp) REVERT: D 169 MET cc_start: 0.8420 (ttp) cc_final: 0.8160 (tmm) REVERT: D 231 ILE cc_start: 0.8509 (mm) cc_final: 0.8205 (tt) REVERT: D 246 GLN cc_start: 0.8119 (mt0) cc_final: 0.7898 (mt0) REVERT: D 259 LEU cc_start: 0.8518 (mt) cc_final: 0.8292 (mp) REVERT: D 263 VAL cc_start: 0.8603 (t) cc_final: 0.8362 (p) REVERT: D 318 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7863 (tttp) REVERT: D 324 ASP cc_start: 0.7637 (m-30) cc_final: 0.7034 (m-30) REVERT: D 392 TYR cc_start: 0.8652 (m-80) cc_final: 0.7812 (m-80) REVERT: D 395 ASN cc_start: 0.7295 (p0) cc_final: 0.6635 (p0) REVERT: D 423 LYS cc_start: 0.8405 (mttm) cc_final: 0.8172 (mtpt) REVERT: D 491 TYR cc_start: 0.7953 (t80) cc_final: 0.7653 (t80) REVERT: D 511 TYR cc_start: 0.8115 (p90) cc_final: 0.7539 (p90) REVERT: D 515 ASP cc_start: 0.6640 (t0) cc_final: 0.6290 (t0) outliers start: 10 outliers final: 8 residues processed: 238 average time/residue: 0.1018 time to fit residues: 33.5690 Evaluate side-chains 231 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 70 optimal weight: 0.2980 chunk 10 optimal weight: 0.0670 overall best weight: 0.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 306 ASN B 314 HIS C 98 GLN D 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104163 restraints weight = 25019.973| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.45 r_work: 0.3149 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11358 Z= 0.089 Angle : 0.463 10.900 15606 Z= 0.239 Chirality : 0.040 0.155 1740 Planarity : 0.004 0.039 1846 Dihedral : 11.696 73.962 2013 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.00 % Allowed : 15.11 % Favored : 83.89 % 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: 0.29 (0.24), residues: 1275 helix: 1.33 (0.31), residues: 294 sheet: -1.06 (0.35), residues: 173 loop : 0.15 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.022 0.001 TYR D 447 PHE 0.016 0.001 PHE D 326 TRP 0.013 0.001 TRP D 509 HIS 0.003 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (11317) covalent geometry : angle 0.45794 / 0.24 (15573) hydrogen bonds : bond 0.03216 / 2.17 ( 362) hydrogen bonds : angle 3.84980 / 2.64 ( 962) metal coordination : bond 0.00416 / 0.28 ( 40) metal coordination : angle 1.56697 / 1.07 ( 33) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.379 Fit side-chains REVERT: A 5 THR cc_start: 0.7994 (m) cc_final: 0.7542 (m) REVERT: A 6 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 122 MET cc_start: 0.8573 (mmt) cc_final: 0.8322 (mmm) REVERT: B 65 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7452 (tm-30) REVERT: B 77 GLU cc_start: 0.7355 (mp0) cc_final: 0.7097 (mp0) REVERT: B 139 LYS cc_start: 0.8165 (tttt) cc_final: 0.7872 (ptmm) REVERT: B 153 MET cc_start: 0.8382 (mmm) cc_final: 0.8020 (mmm) REVERT: B 154 TYR cc_start: 0.8084 (m-80) cc_final: 0.7785 (m-80) REVERT: B 212 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7990 (mtt-85) REVERT: B 295 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 310 ARG cc_start: 0.8407 (mtp180) cc_final: 0.8149 (mtp180) REVERT: B 315 MET cc_start: 0.8443 (tpp) cc_final: 0.8192 (tpp) REVERT: B 324 ASP cc_start: 0.7103 (m-30) cc_final: 0.6683 (m-30) REVERT: B 325 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7580 (mmmm) REVERT: B 347 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 349 LYS cc_start: 0.8361 (mttt) cc_final: 0.7740 (mttt) REVERT: B 351 TYR cc_start: 0.8497 (m-80) cc_final: 0.7881 (m-80) REVERT: B 352 ASP cc_start: 0.6848 (t0) cc_final: 0.6258 (t0) REVERT: B 398 VAL cc_start: 0.8538 (t) cc_final: 0.8292 (m) REVERT: B 421 VAL cc_start: 0.7801 (t) cc_final: 0.7556 (t) REVERT: B 491 TYR cc_start: 0.7587 (t80) cc_final: 0.7374 (t80) REVERT: B 492 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7389 (mtm110) REVERT: B 520 TRP cc_start: 0.7823 (m100) cc_final: 0.7368 (m100) REVERT: D 61 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7421 (mtpt) REVERT: D 169 MET cc_start: 0.8441 (ttp) cc_final: 0.8188 (tmm) REVERT: D 231 ILE cc_start: 0.8547 (mm) cc_final: 0.8230 (tt) REVERT: D 259 LEU cc_start: 0.8517 (mt) cc_final: 0.8278 (mp) REVERT: D 263 VAL cc_start: 0.8599 (t) cc_final: 0.8364 (p) REVERT: D 318 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7857 (tttp) REVERT: D 324 ASP cc_start: 0.7604 (m-30) cc_final: 0.6995 (m-30) REVERT: D 339 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7936 (mttt) REVERT: D 392 TYR cc_start: 0.8518 (m-80) cc_final: 0.7980 (m-80) REVERT: D 395 ASN cc_start: 0.7266 (p0) cc_final: 0.6621 (p0) REVERT: D 423 LYS cc_start: 0.8447 (mttm) cc_final: 0.8164 (mtpt) REVERT: D 491 TYR cc_start: 0.7938 (t80) cc_final: 0.7629 (t80) REVERT: D 511 TYR cc_start: 0.8064 (p90) cc_final: 0.7489 (p90) REVERT: D 515 ASP cc_start: 0.6705 (t0) cc_final: 0.6355 (t0) outliers start: 11 outliers final: 9 residues processed: 229 average time/residue: 0.1197 time to fit residues: 37.6562 Evaluate side-chains 231 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 5 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 76 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN C 98 GLN D 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103796 restraints weight = 20941.929| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.19 r_work: 0.3154 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11358 Z= 0.124 Angle : 0.482 10.585 15606 Z= 0.250 Chirality : 0.041 0.172 1740 Planarity : 0.004 0.040 1846 Dihedral : 11.687 73.967 2013 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.63 % Allowed : 15.75 % Favored : 83.62 % 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: 0.26 (0.24), residues: 1275 helix: 1.28 (0.31), residues: 294 sheet: -1.03 (0.35), residues: 173 loop : 0.13 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 205 TYR 0.022 0.001 TYR D 447 PHE 0.013 0.001 PHE D 326 TRP 0.013 0.001 TRP D 509 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (11317) covalent geometry : angle 0.47599 / 0.25 (15573) hydrogen bonds : bond 0.03476 / 2.33 ( 362) hydrogen bonds : angle 3.90963 / 2.68 ( 962) metal coordination : bond 0.00620 / 0.43 ( 40) metal coordination : angle 1.66682 / 1.13 ( 33) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.286 Fit side-chains REVERT: A 5 THR cc_start: 0.7998 (m) cc_final: 0.7539 (m) REVERT: A 6 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7675 (tp30) REVERT: B 31 THR cc_start: 0.8210 (m) cc_final: 0.7961 (t) REVERT: B 65 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7401 (tm-30) REVERT: B 77 GLU cc_start: 0.7332 (mp0) cc_final: 0.7077 (mp0) REVERT: B 139 LYS cc_start: 0.8150 (tttt) cc_final: 0.7869 (ptmm) REVERT: B 153 MET cc_start: 0.8381 (mmm) cc_final: 0.8017 (mmm) REVERT: B 154 TYR cc_start: 0.8087 (m-80) cc_final: 0.7768 (m-80) REVERT: B 212 ARG cc_start: 0.8246 (mtt90) cc_final: 0.8011 (mtt-85) REVERT: B 295 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 310 ARG cc_start: 0.8331 (mtp180) cc_final: 0.8068 (mtp180) REVERT: B 315 MET cc_start: 0.8413 (tpp) cc_final: 0.8158 (tpp) REVERT: B 324 ASP cc_start: 0.7053 (m-30) cc_final: 0.6643 (m-30) REVERT: B 325 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7529 (mmmm) REVERT: B 347 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 349 LYS cc_start: 0.8358 (mttt) cc_final: 0.7853 (mttt) REVERT: B 352 ASP cc_start: 0.6840 (t0) cc_final: 0.6250 (t0) REVERT: B 398 VAL cc_start: 0.8519 (t) cc_final: 0.8249 (p) REVERT: B 421 VAL cc_start: 0.7766 (t) cc_final: 0.7508 (t) REVERT: B 491 TYR cc_start: 0.7589 (t80) cc_final: 0.7367 (t80) REVERT: B 492 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7374 (mtm110) REVERT: B 520 TRP cc_start: 0.7862 (m100) cc_final: 0.7440 (m100) REVERT: D 35 THR cc_start: 0.7806 (t) cc_final: 0.7334 (p) REVERT: D 61 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7423 (mtpt) REVERT: D 169 MET cc_start: 0.8450 (ttp) cc_final: 0.8185 (tmm) REVERT: D 231 ILE cc_start: 0.8544 (mm) cc_final: 0.8236 (tt) REVERT: D 259 LEU cc_start: 0.8508 (mt) cc_final: 0.8281 (mp) REVERT: D 263 VAL cc_start: 0.8610 (t) cc_final: 0.8375 (p) REVERT: D 318 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7882 (tttp) REVERT: D 324 ASP cc_start: 0.7523 (m-30) cc_final: 0.7132 (m-30) REVERT: D 392 TYR cc_start: 0.8531 (m-80) cc_final: 0.7998 (m-80) REVERT: D 395 ASN cc_start: 0.7281 (p0) cc_final: 0.6673 (p0) REVERT: D 423 LYS cc_start: 0.8410 (mttm) cc_final: 0.8126 (mtpt) REVERT: D 491 TYR cc_start: 0.7947 (t80) cc_final: 0.7618 (t80) REVERT: D 511 TYR cc_start: 0.7995 (p90) cc_final: 0.7393 (p90) REVERT: D 515 ASP cc_start: 0.6701 (t0) cc_final: 0.6367 (t0) outliers start: 7 outliers final: 7 residues processed: 220 average time/residue: 0.1204 time to fit residues: 36.4794 Evaluate side-chains 225 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 chunk 93 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN C 98 GLN D 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102211 restraints weight = 26155.408| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.50 r_work: 0.3116 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11358 Z= 0.145 Angle : 0.494 10.902 15606 Z= 0.256 Chirality : 0.042 0.156 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.679 74.052 2013 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.81 % Allowed : 15.48 % Favored : 83.71 % 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: 0.23 (0.24), residues: 1275 helix: 1.22 (0.31), residues: 294 sheet: -0.94 (0.35), residues: 183 loop : 0.11 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.023 0.001 TYR D 447 PHE 0.025 0.002 PHE B 444 TRP 0.010 0.001 TRP D 509 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (11317) covalent geometry : angle 0.48702 / 0.26 (15573) hydrogen bonds : bond 0.03666 / 2.44 ( 362) hydrogen bonds : angle 3.99086 / 2.74 ( 962) metal coordination : bond 0.00720 / 0.50 ( 40) metal coordination : angle 1.80776 / 1.21 ( 33) Misc. bond : bond 0.00027 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.76 seconds wall clock time: 67 minutes 40.58 seconds (4060.58 seconds total)