Starting phenix.real_space_refine on Fri Jul 3 00:55:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrk_73369/07_2026/9yrk_73369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrk_73369/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9yrk_73369/07_2026/9yrk_73369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrk_73369/07_2026/9yrk_73369.map" model { file = "/net/cci-nas-00/data/ceres_data/9yrk_73369/07_2026/9yrk_73369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrk_73369/07_2026/9yrk_73369.cif" } 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-dev-6108/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: 3.21, per 1000 atoms: 0.29 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: 0.94 Conformation dependent library (CDL) restraints added in 462.0 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: 1.01 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: 1.85 Time building geometry restraints manager: 1.02 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: 15452 2.54 - 5.08: 105 5.08 - 7.62: 13 7.62 - 10.16: 2 10.16 - 12.69: 1 Bond angle restraints: 15573 Sorted by residual: 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=" 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 angle pdb=" C CYS B 208 " pdb=" N LEU B 209 " pdb=" CA LEU B 209 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C LEU D 149 " pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 120.33 123.04 -2.71 8.00e-01 1.56e+00 1.14e+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: 1625 0.090 - 0.180: 111 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: 3.410 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- 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= 0.206 Angle : 0.601 12.695 15606 Z= 0.355 Chirality : 0.047 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 0.00410 / 0.20 (11317) covalent geometry : angle 0.59447 / 0.35 (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 : 0.401 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: 0.1224 time to fit residues: 46.6818 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 : 0.248 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102265 restraints weight = 21821.326| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.27 r_work: 0.3121 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 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: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1005 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 5.375 15606 Z= 0.268 Chirality : 0.042 0.155 1740 Planarity : 0.005 0.050 1846 Dihedral : 11.963 74.561 2013 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.90 % Allowed : 10.86 % Favored : 88.24 % 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: 0.56 (0.31), residues: 296 sheet: -1.11 (0.36), residues: 173 loop : 0.05 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 391 TYR 0.018 0.001 TYR D 370 PHE 0.036 0.002 PHE B 350 TRP 0.015 0.001 TRP B 348 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11317) covalent geometry : angle 0.49542 / 0.27 (15573) hydrogen bonds : bond 0.04676 / 3.12 ( 362) hydrogen bonds : angle 4.54996 / 3.13 ( 962) metal coordination : bond 0.00897 / 0.62 ( 40) metal coordination : angle 2.19812 / 1.42 ( 33) Misc. bond : bond 0.00571 / 0.30 ( 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 261 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7521 (tp30) REVERT: A 56 THR cc_start: 0.8333 (p) cc_final: 0.8100 (p) REVERT: A 58 THR cc_start: 0.8477 (t) cc_final: 0.8105 (t) REVERT: A 122 MET cc_start: 0.8583 (mmt) cc_final: 0.8108 (mmm) REVERT: B 13 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7792 (mtmt) REVERT: B 71 ASN cc_start: 0.7821 (m110) cc_final: 0.7611 (t0) REVERT: B 77 GLU cc_start: 0.7394 (mp0) cc_final: 0.7159 (mp0) REVERT: B 98 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7838 (mtm110) REVERT: B 122 THR cc_start: 0.8325 (m) cc_final: 0.8019 (p) REVERT: B 139 LYS cc_start: 0.8152 (tttt) cc_final: 0.7886 (ptmm) REVERT: B 153 MET cc_start: 0.8493 (mmm) cc_final: 0.8215 (mmm) REVERT: B 154 TYR cc_start: 0.8190 (m-80) cc_final: 0.7837 (m-80) REVERT: B 195 MET cc_start: 0.8278 (mtt) cc_final: 0.8028 (mtt) REVERT: B 212 ARG cc_start: 0.8300 (mtt90) cc_final: 0.8087 (mtt-85) REVERT: B 284 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8108 (mm-30) REVERT: B 304 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7902 (mmtt) REVERT: B 315 MET cc_start: 0.8362 (tpp) cc_final: 0.8120 (tpp) REVERT: B 324 ASP cc_start: 0.7136 (m-30) cc_final: 0.6592 (m-30) REVERT: B 325 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7551 (mtmm) REVERT: B 347 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 349 LYS cc_start: 0.8298 (mttt) cc_final: 0.7782 (mttt) REVERT: B 352 ASP cc_start: 0.6805 (t0) cc_final: 0.6096 (t0) REVERT: B 398 VAL cc_start: 0.8550 (t) cc_final: 0.8289 (p) REVERT: B 404 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7179 (mtm180) REVERT: B 421 VAL cc_start: 0.7784 (t) cc_final: 0.7521 (t) REVERT: B 491 TYR cc_start: 0.7627 (t80) cc_final: 0.7277 (t80) REVERT: B 492 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7483 (mtm110) REVERT: C 6 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7730 (mm-30) REVERT: C 51 THR cc_start: 0.8627 (t) cc_final: 0.8378 (p) REVERT: C 56 THR cc_start: 0.8380 (p) cc_final: 0.8108 (p) REVERT: D 61 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7444 (mtpt) REVERT: D 169 MET cc_start: 0.8407 (ttp) cc_final: 0.8167 (tmm) REVERT: D 211 ASP cc_start: 0.7847 (t0) cc_final: 0.7470 (t0) REVERT: D 231 ILE cc_start: 0.8553 (mm) cc_final: 0.8287 (tt) REVERT: D 246 GLN cc_start: 0.8170 (mt0) cc_final: 0.7834 (mt0) REVERT: D 259 LEU cc_start: 0.8591 (mt) cc_final: 0.8323 (mp) REVERT: D 263 VAL cc_start: 0.8611 (t) cc_final: 0.8349 (p) REVERT: D 295 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 310 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7692 (mtp180) REVERT: D 311 LYS cc_start: 0.8391 (tttt) cc_final: 0.8145 (ttmm) REVERT: D 318 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7870 (ttpt) REVERT: D 324 ASP cc_start: 0.7832 (m-30) cc_final: 0.7263 (m-30) REVERT: D 326 PHE cc_start: 0.8301 (m-80) cc_final: 0.7832 (m-10) REVERT: D 331 ASP cc_start: 0.7642 (t0) cc_final: 0.7173 (t0) REVERT: D 423 LYS cc_start: 0.8405 (mttm) cc_final: 0.8136 (mtpp) REVERT: D 491 TYR cc_start: 0.7973 (t80) cc_final: 0.7725 (t80) outliers start: 10 outliers final: 4 residues processed: 257 average time/residue: 0.1179 time to fit residues: 40.4915 Evaluate side-chains 243 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 0.7980 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 0.0770 chunk 104 optimal weight: 0.5980 overall best weight: 0.2712 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102626 restraints weight = 24832.278| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.42 r_work: 0.3126 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 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 = 0.2956 r_free = 0.2956 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: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11358 Z= 0.108 Angle : 0.478 6.634 15606 Z= 0.251 Chirality : 0.041 0.159 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.887 74.050 2013 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.72 % Allowed : 11.67 % Favored : 87.60 % 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: 0.10 (0.24), residues: 1275 helix: 0.85 (0.32), residues: 294 sheet: -0.98 (0.37), residues: 173 loop : 0.12 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.014 0.001 TYR B 420 PHE 0.018 0.001 PHE D 444 TRP 0.021 0.001 TRP B 348 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11317) covalent geometry : angle 0.46974 / 0.25 (15573) hydrogen bonds : bond 0.03989 / 2.66 ( 362) hydrogen bonds : angle 4.25989 / 2.93 ( 962) metal coordination : bond 0.00665 / 0.47 ( 40) metal coordination : angle 1.98601 / 1.31 ( 33) Misc. bond : bond 0.00333 / 0.18 ( 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 251 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 243 time to evaluate : 0.324 Fit side-chains REVERT: A 6 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7599 (tp30) REVERT: A 58 THR cc_start: 0.8429 (t) cc_final: 0.8046 (t) REVERT: B 71 ASN cc_start: 0.7835 (m110) cc_final: 0.7562 (t0) REVERT: B 77 GLU cc_start: 0.7356 (mp0) cc_final: 0.7116 (mp0) REVERT: B 122 THR cc_start: 0.8347 (m) cc_final: 0.8043 (p) REVERT: B 139 LYS cc_start: 0.8138 (tttt) cc_final: 0.7849 (ptmm) REVERT: B 153 MET cc_start: 0.8466 (mmm) cc_final: 0.8226 (mmm) REVERT: B 154 TYR cc_start: 0.8141 (m-80) cc_final: 0.7742 (m-80) REVERT: B 195 MET cc_start: 0.8260 (mtt) cc_final: 0.8029 (mtm) REVERT: B 212 ARG cc_start: 0.8290 (mtt90) cc_final: 0.8066 (mtt-85) REVERT: B 284 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8127 (mm-30) REVERT: B 315 MET cc_start: 0.8387 (tpp) cc_final: 0.8146 (tpp) REVERT: B 324 ASP cc_start: 0.7141 (m-30) cc_final: 0.6634 (m-30) REVERT: B 339 LYS cc_start: 0.7589 (mtmm) cc_final: 0.7380 (mtpp) REVERT: B 347 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 349 LYS cc_start: 0.8300 (mttt) cc_final: 0.7757 (mttt) REVERT: B 352 ASP cc_start: 0.6835 (t0) cc_final: 0.6120 (t0) REVERT: B 398 VAL cc_start: 0.8545 (t) cc_final: 0.8298 (p) REVERT: B 404 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7218 (mtm180) REVERT: B 421 VAL cc_start: 0.7793 (t) cc_final: 0.7543 (t) REVERT: B 491 TYR cc_start: 0.7640 (t80) cc_final: 0.7309 (t80) REVERT: B 492 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7456 (mtm110) REVERT: C 6 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 51 THR cc_start: 0.8643 (t) cc_final: 0.8385 (p) REVERT: C 56 THR cc_start: 0.8378 (p) cc_final: 0.8095 (p) REVERT: D 35 THR cc_start: 0.7535 (m) cc_final: 0.7026 (p) REVERT: D 61 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7416 (mtpt) REVERT: D 211 ASP cc_start: 0.7881 (t0) cc_final: 0.7566 (t0) REVERT: D 231 ILE cc_start: 0.8562 (mm) cc_final: 0.8282 (tt) REVERT: D 246 GLN cc_start: 0.8174 (mt0) cc_final: 0.7850 (mt0) REVERT: D 259 LEU cc_start: 0.8558 (mt) cc_final: 0.8304 (mp) REVERT: D 263 VAL cc_start: 0.8608 (t) cc_final: 0.8342 (p) REVERT: D 295 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8334 (mt-10) REVERT: D 311 LYS cc_start: 0.8372 (tttt) cc_final: 0.8122 (ttmm) REVERT: D 318 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7863 (ttpt) REVERT: D 324 ASP cc_start: 0.7884 (m-30) cc_final: 0.6916 (m-30) REVERT: D 326 PHE cc_start: 0.8206 (m-80) cc_final: 0.8003 (m-10) REVERT: D 423 LYS cc_start: 0.8426 (mttm) cc_final: 0.8101 (mtpp) REVERT: D 491 TYR cc_start: 0.7965 (t80) cc_final: 0.7637 (t80) REVERT: D 511 TYR cc_start: 0.8053 (p90) cc_final: 0.7233 (p90) REVERT: D 515 ASP cc_start: 0.6827 (t0) cc_final: 0.6504 (t0) outliers start: 8 outliers final: 6 residues processed: 246 average time/residue: 0.1227 time to fit residues: 40.1211 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 314 HIS C 40 ASN C 98 GLN D 108 GLN D 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101343 restraints weight = 26101.898| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.53 r_work: 0.3096 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1463 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= 0.162 Angle : 0.496 7.341 15606 Z= 0.260 Chirality : 0.042 0.151 1740 Planarity : 0.004 0.043 1846 Dihedral : 11.868 74.070 2013 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.36 % Allowed : 12.13 % 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: 0.10 (0.24), residues: 1275 helix: 0.86 (0.31), residues: 294 sheet: -0.94 (0.35), residues: 183 loop : 0.12 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 84 TYR 0.018 0.001 TYR B 420 PHE 0.024 0.002 PHE B 444 TRP 0.011 0.001 TRP B 520 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11317) covalent geometry : angle 0.48821 / 0.26 (15573) hydrogen bonds : bond 0.04117 / 2.74 ( 362) hydrogen bonds : angle 4.23409 / 2.92 ( 962) metal coordination : bond 0.00879 / 0.62 ( 40) metal coordination : angle 1.98006 / 1.32 ( 33) Misc. bond : bond 0.00161 / 0.08 ( 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 255 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7597 (tp30) REVERT: B 65 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7490 (tm-30) REVERT: B 71 ASN cc_start: 0.7810 (m110) cc_final: 0.7576 (t0) REVERT: B 77 GLU cc_start: 0.7465 (mp0) cc_final: 0.7209 (mp0) REVERT: B 139 LYS cc_start: 0.8140 (tttt) cc_final: 0.7866 (ptmm) REVERT: B 153 MET cc_start: 0.8451 (mmm) cc_final: 0.8013 (mmm) REVERT: B 154 TYR cc_start: 0.8187 (m-80) cc_final: 0.7807 (m-80) REVERT: B 212 ARG cc_start: 0.8310 (mtt90) cc_final: 0.8089 (mtt-85) REVERT: B 284 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8158 (mm-30) REVERT: B 295 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8384 (mt-10) REVERT: B 304 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7905 (mmtt) REVERT: B 315 MET cc_start: 0.8369 (tpp) cc_final: 0.8136 (tpp) REVERT: B 324 ASP cc_start: 0.7175 (m-30) cc_final: 0.6667 (m-30) REVERT: B 339 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7317 (mtmm) REVERT: B 347 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 349 LYS cc_start: 0.8357 (mttt) cc_final: 0.7826 (mttt) REVERT: B 352 ASP cc_start: 0.6821 (t0) cc_final: 0.6090 (t0) REVERT: B 398 VAL cc_start: 0.8585 (t) cc_final: 0.8332 (p) REVERT: B 404 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7229 (mtm180) REVERT: B 421 VAL cc_start: 0.7835 (t) cc_final: 0.7571 (t) REVERT: B 491 TYR cc_start: 0.7689 (t80) cc_final: 0.7346 (t80) REVERT: B 492 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7481 (mtm110) REVERT: C 6 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 51 THR cc_start: 0.8653 (t) cc_final: 0.8390 (p) REVERT: C 56 THR cc_start: 0.8333 (p) cc_final: 0.8051 (p) REVERT: D 35 THR cc_start: 0.7551 (m) cc_final: 0.7041 (p) REVERT: D 61 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7453 (mtpt) REVERT: D 169 MET cc_start: 0.8475 (ttp) cc_final: 0.8199 (tmm) REVERT: D 211 ASP cc_start: 0.7878 (t0) cc_final: 0.7450 (t0) REVERT: D 231 ILE cc_start: 0.8565 (mm) cc_final: 0.8289 (tt) REVERT: D 246 GLN cc_start: 0.8189 (mt0) cc_final: 0.7885 (mt0) REVERT: D 259 LEU cc_start: 0.8581 (mt) cc_final: 0.8331 (mp) REVERT: D 263 VAL cc_start: 0.8583 (t) cc_final: 0.8301 (p) REVERT: D 295 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8324 (mt-10) REVERT: D 318 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7876 (ttpt) REVERT: D 324 ASP cc_start: 0.7876 (m-30) cc_final: 0.7236 (m-30) REVERT: D 326 PHE cc_start: 0.8257 (m-80) cc_final: 0.8007 (m-10) REVERT: D 352 ASP cc_start: 0.6976 (m-30) cc_final: 0.6722 (m-30) REVERT: D 395 ASN cc_start: 0.7389 (p0) cc_final: 0.6906 (p0) REVERT: D 491 TYR cc_start: 0.7982 (t80) cc_final: 0.7667 (t80) outliers start: 15 outliers final: 8 residues processed: 245 average time/residue: 0.1130 time to fit residues: 36.8842 Evaluate side-chains 242 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain B residue 215 THR 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 172 ASP Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 0.0470 chunk 77 optimal weight: 0.0870 chunk 78 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 160 ASN 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 = 0.3690 r_free = 0.3690 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103087 restraints weight = 23839.105| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.37 r_work: 0.3130 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11358 Z= 0.100 Angle : 0.459 7.296 15606 Z= 0.241 Chirality : 0.041 0.181 1740 Planarity : 0.004 0.040 1846 Dihedral : 11.803 73.913 2013 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.90 % Allowed : 13.21 % Favored : 85.88 % 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: 1.08 (0.31), residues: 294 sheet: -0.92 (0.37), residues: 173 loop : 0.14 (0.23), residues: 808 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 227 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11317) covalent geometry : angle 0.45212 / 0.24 (15573) hydrogen bonds : bond 0.03581 / 2.40 ( 362) hydrogen bonds : angle 4.04306 / 2.79 ( 962) metal coordination : bond 0.00532 / 0.37 ( 40) metal coordination : angle 1.78135 / 1.19 ( 33) Misc. bond : bond 0.00064 / 0.03 ( 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 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7641 (tp30) REVERT: B 65 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7471 (tm-30) REVERT: B 77 GLU cc_start: 0.7356 (mp0) cc_final: 0.7105 (mp0) REVERT: B 139 LYS cc_start: 0.8135 (tttt) cc_final: 0.7841 (ptmm) REVERT: B 153 MET cc_start: 0.8457 (mmm) cc_final: 0.8015 (mmm) REVERT: B 154 TYR cc_start: 0.8122 (m-80) cc_final: 0.7795 (m-80) REVERT: B 212 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8032 (mtt-85) REVERT: B 295 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8351 (mt-10) REVERT: B 315 MET cc_start: 0.8417 (tpp) cc_final: 0.8186 (tpp) REVERT: B 324 ASP cc_start: 0.7113 (m-30) cc_final: 0.6665 (m-30) REVERT: B 325 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7441 (mmmm) REVERT: B 339 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7357 (mtmm) REVERT: B 347 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 349 LYS cc_start: 0.8290 (mttt) cc_final: 0.7774 (mttt) REVERT: B 352 ASP cc_start: 0.6787 (t0) cc_final: 0.6072 (t0) REVERT: B 398 VAL cc_start: 0.8552 (t) cc_final: 0.8293 (p) REVERT: B 404 ARG cc_start: 0.7434 (mtm180) cc_final: 0.7051 (mtm180) REVERT: B 421 VAL cc_start: 0.7795 (t) cc_final: 0.7542 (t) REVERT: B 491 TYR cc_start: 0.7647 (t80) cc_final: 0.7352 (t80) REVERT: B 492 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7393 (mtm110) REVERT: C 6 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 40 ASN cc_start: 0.8843 (t0) cc_final: 0.8584 (t0) REVERT: C 51 THR cc_start: 0.8635 (t) cc_final: 0.8369 (p) REVERT: C 56 THR cc_start: 0.8329 (p) cc_final: 0.8023 (p) REVERT: C 101 THR cc_start: 0.8173 (t) cc_final: 0.7944 (m) REVERT: D 35 THR cc_start: 0.7540 (m) cc_final: 0.7068 (p) REVERT: D 49 MET cc_start: 0.8233 (mmm) cc_final: 0.8027 (mmm) REVERT: D 61 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7405 (mtpt) REVERT: D 169 MET cc_start: 0.8449 (ttp) cc_final: 0.8172 (tmm) REVERT: D 231 ILE cc_start: 0.8558 (mm) cc_final: 0.8272 (tt) REVERT: D 246 GLN cc_start: 0.8161 (mt0) cc_final: 0.7917 (mt0) REVERT: D 259 LEU cc_start: 0.8558 (mt) cc_final: 0.8323 (mp) REVERT: D 263 VAL cc_start: 0.8581 (t) cc_final: 0.8306 (p) REVERT: D 295 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8278 (mt-10) REVERT: D 311 LYS cc_start: 0.8319 (tttt) cc_final: 0.7823 (ttmm) REVERT: D 318 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7839 (ttpt) REVERT: D 324 ASP cc_start: 0.7812 (m-30) cc_final: 0.6910 (m-30) REVERT: D 326 PHE cc_start: 0.8231 (m-80) cc_final: 0.8011 (m-10) REVERT: D 395 ASN cc_start: 0.7360 (p0) cc_final: 0.6866 (p0) REVERT: D 491 TYR cc_start: 0.7933 (t80) cc_final: 0.7600 (t80) REVERT: D 511 TYR cc_start: 0.8070 (p90) cc_final: 0.7275 (p90) outliers start: 10 outliers final: 5 residues processed: 240 average time/residue: 0.1131 time to fit residues: 36.6301 Evaluate side-chains 236 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 231 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 D residue 172 ASP 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: 3.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 94 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 314 HIS C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102691 restraints weight = 26347.363| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.52 r_work: 0.3122 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 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: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11358 Z= 0.106 Angle : 0.466 9.081 15606 Z= 0.242 Chirality : 0.041 0.149 1740 Planarity : 0.004 0.041 1846 Dihedral : 11.759 73.953 2013 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.00 % Allowed : 13.67 % Favored : 85.34 % 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: 0.24 (0.24), residues: 1275 helix: 1.08 (0.31), residues: 294 sheet: -0.90 (0.36), residues: 173 loop : 0.16 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 53 TYR 0.019 0.001 TYR D 447 PHE 0.024 0.001 PHE D 444 TRP 0.007 0.001 TRP B 385 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11317) covalent geometry : angle 0.45958 / 0.24 (15573) hydrogen bonds : bond 0.03526 / 2.36 ( 362) hydrogen bonds : angle 4.00991 / 2.77 ( 962) metal coordination : bond 0.00556 / 0.38 ( 40) metal coordination : angle 1.73991 / 1.17 ( 33) Misc. bond : bond 0.00055 / 0.03 ( 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 250 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8019 (m) cc_final: 0.7572 (m) REVERT: A 6 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7696 (tp30) REVERT: B 65 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7454 (tm-30) REVERT: B 77 GLU cc_start: 0.7375 (mp0) cc_final: 0.7112 (mp0) REVERT: B 139 LYS cc_start: 0.8160 (tttt) cc_final: 0.7882 (ptmm) REVERT: B 153 MET cc_start: 0.8430 (mmm) cc_final: 0.8043 (mmm) REVERT: B 154 TYR cc_start: 0.8136 (m-80) cc_final: 0.7808 (m-80) REVERT: B 212 ARG cc_start: 0.8270 (mtt90) cc_final: 0.8040 (mtt-85) REVERT: B 315 MET cc_start: 0.8438 (tpp) cc_final: 0.8205 (tpp) REVERT: B 324 ASP cc_start: 0.7116 (m-30) cc_final: 0.6609 (m-30) REVERT: B 339 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7371 (mtmm) REVERT: B 347 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 349 LYS cc_start: 0.8336 (mttt) cc_final: 0.7717 (mttt) REVERT: B 351 TYR cc_start: 0.8502 (m-80) cc_final: 0.7887 (m-80) REVERT: B 352 ASP cc_start: 0.6848 (t0) cc_final: 0.6107 (t0) REVERT: B 398 VAL cc_start: 0.8579 (t) cc_final: 0.8325 (p) REVERT: B 404 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7243 (mtm180) REVERT: B 421 VAL cc_start: 0.7812 (t) cc_final: 0.7560 (t) REVERT: B 491 TYR cc_start: 0.7654 (t80) cc_final: 0.7367 (t80) REVERT: B 492 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7434 (mtm110) REVERT: C 51 THR cc_start: 0.8636 (t) cc_final: 0.8378 (p) REVERT: C 56 THR cc_start: 0.8334 (p) cc_final: 0.8040 (p) REVERT: C 101 THR cc_start: 0.8172 (t) cc_final: 0.7953 (m) REVERT: D 35 THR cc_start: 0.7554 (m) cc_final: 0.7084 (p) REVERT: D 61 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7425 (mtpt) REVERT: D 169 MET cc_start: 0.8472 (ttp) cc_final: 0.8200 (tmm) REVERT: D 231 ILE cc_start: 0.8554 (mm) cc_final: 0.8264 (tt) REVERT: D 246 GLN cc_start: 0.8159 (mt0) cc_final: 0.7924 (mt0) REVERT: D 259 LEU cc_start: 0.8551 (mt) cc_final: 0.8320 (mp) REVERT: D 263 VAL cc_start: 0.8602 (t) cc_final: 0.8345 (p) REVERT: D 295 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 318 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7842 (ttpt) REVERT: D 324 ASP cc_start: 0.7821 (m-30) cc_final: 0.7099 (m-30) REVERT: D 395 ASN cc_start: 0.7401 (p0) cc_final: 0.6900 (p0) REVERT: D 491 TYR cc_start: 0.7958 (t80) cc_final: 0.7610 (t80) REVERT: D 511 TYR cc_start: 0.8066 (p90) cc_final: 0.7328 (p90) outliers start: 11 outliers final: 9 residues processed: 243 average time/residue: 0.1120 time to fit residues: 37.0175 Evaluate side-chains 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 495 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.131834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101628 restraints weight = 24825.802| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.45 r_work: 0.3110 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11358 Z= 0.172 Angle : 0.501 8.413 15606 Z= 0.262 Chirality : 0.042 0.145 1740 Planarity : 0.004 0.043 1846 Dihedral : 11.755 74.115 2013 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.90 % Allowed : 14.12 % 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: 0.19 (0.24), residues: 1275 helix: 1.01 (0.31), residues: 294 sheet: -0.97 (0.34), residues: 195 loop : 0.19 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.021 0.001 TYR D 447 PHE 0.042 0.002 PHE D 326 TRP 0.010 0.001 TRP B 520 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (11317) covalent geometry : angle 0.49401 / 0.26 (15573) hydrogen bonds : bond 0.03934 / 2.62 ( 362) hydrogen bonds : angle 4.11142 / 2.83 ( 962) metal coordination : bond 0.00884 / 0.62 ( 40) metal coordination : angle 1.91473 / 1.28 ( 33) Misc. bond : bond 0.00007 / 0.00 ( 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 245 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.359 Fit side-chains REVERT: A 5 THR cc_start: 0.8052 (m) cc_final: 0.7600 (m) REVERT: A 6 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7723 (tp30) REVERT: B 65 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7471 (tm-30) REVERT: B 77 GLU cc_start: 0.7417 (mp0) cc_final: 0.7164 (mp0) REVERT: B 139 LYS cc_start: 0.8160 (tttt) cc_final: 0.7884 (ptmm) REVERT: B 153 MET cc_start: 0.8405 (mmm) cc_final: 0.8037 (mmm) REVERT: B 154 TYR cc_start: 0.8148 (m-80) cc_final: 0.7791 (m-80) REVERT: B 212 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8066 (mtt-85) REVERT: B 295 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 315 MET cc_start: 0.8437 (tpp) cc_final: 0.8204 (tpp) REVERT: B 324 ASP cc_start: 0.7118 (m-30) cc_final: 0.6694 (m-30) REVERT: B 325 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7519 (mmmm) REVERT: B 339 LYS cc_start: 0.7649 (mtmm) cc_final: 0.7409 (mtmm) REVERT: B 347 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 349 LYS cc_start: 0.8378 (mttt) cc_final: 0.7855 (mttt) REVERT: B 352 ASP cc_start: 0.6868 (t0) cc_final: 0.6114 (t0) REVERT: B 398 VAL cc_start: 0.8552 (t) cc_final: 0.8292 (p) REVERT: B 421 VAL cc_start: 0.7839 (t) cc_final: 0.7582 (t) REVERT: B 491 TYR cc_start: 0.7670 (t80) cc_final: 0.7361 (t80) REVERT: B 492 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7461 (mtm110) REVERT: B 520 TRP cc_start: 0.7883 (m100) cc_final: 0.7413 (m100) REVERT: C 51 THR cc_start: 0.8680 (t) cc_final: 0.8389 (p) REVERT: C 56 THR cc_start: 0.8325 (p) cc_final: 0.8046 (p) REVERT: C 101 THR cc_start: 0.8186 (t) cc_final: 0.7963 (m) REVERT: D 35 THR cc_start: 0.7554 (m) cc_final: 0.7084 (p) REVERT: D 61 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7440 (mtpt) REVERT: D 169 MET cc_start: 0.8475 (ttp) cc_final: 0.8205 (tmm) REVERT: D 211 ASP cc_start: 0.7871 (t0) cc_final: 0.7482 (t0) REVERT: D 231 ILE cc_start: 0.8556 (mm) cc_final: 0.8280 (tt) REVERT: D 246 GLN cc_start: 0.8162 (mt0) cc_final: 0.7932 (mt0) REVERT: D 259 LEU cc_start: 0.8557 (mt) cc_final: 0.8329 (mp) REVERT: D 263 VAL cc_start: 0.8584 (t) cc_final: 0.8310 (p) REVERT: D 295 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 318 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7854 (ttpt) REVERT: D 324 ASP cc_start: 0.7840 (m-30) cc_final: 0.7313 (m-30) REVERT: D 392 TYR cc_start: 0.8657 (m-80) cc_final: 0.7758 (m-80) REVERT: D 395 ASN cc_start: 0.7314 (p0) cc_final: 0.6777 (p0) REVERT: D 423 LYS cc_start: 0.8427 (mttm) cc_final: 0.8104 (mtpp) REVERT: D 491 TYR cc_start: 0.7974 (t80) cc_final: 0.7623 (t80) REVERT: D 511 TYR cc_start: 0.8173 (p90) cc_final: 0.7486 (p90) outliers start: 10 outliers final: 10 residues processed: 241 average time/residue: 0.1180 time to fit residues: 38.5352 Evaluate side-chains 242 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 232 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 14 VAL 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 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: 0.0670 chunk 21 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 314 HIS 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 = 0.132112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102746 restraints weight = 21091.513| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.19 r_work: 0.3136 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11358 Z= 0.140 Angle : 0.491 8.679 15606 Z= 0.255 Chirality : 0.041 0.148 1740 Planarity : 0.004 0.072 1846 Dihedral : 11.744 73.975 2013 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.00 % Allowed : 14.48 % Favored : 84.52 % 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: 0.19 (0.24), residues: 1275 helix: 1.03 (0.31), residues: 294 sheet: -1.01 (0.34), residues: 195 loop : 0.19 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 98 TYR 0.022 0.001 TYR D 447 PHE 0.031 0.002 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 0.00337 / 0.14 (11317) covalent geometry : angle 0.48453 / 0.25 (15573) hydrogen bonds : bond 0.03758 / 2.50 ( 362) hydrogen bonds : angle 4.05873 / 2.80 ( 962) metal coordination : bond 0.00682 / 0.47 ( 40) metal coordination : angle 1.83716 / 1.23 ( 33) Misc. bond : bond 0.00033 / 0.02 ( 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 241 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.388 Fit side-chains REVERT: A 5 THR cc_start: 0.8025 (m) cc_final: 0.7545 (m) REVERT: A 6 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7677 (tp30) REVERT: B 77 GLU cc_start: 0.7308 (mp0) cc_final: 0.7041 (mp0) REVERT: B 139 LYS cc_start: 0.8137 (tttt) cc_final: 0.7838 (ptmm) REVERT: B 153 MET cc_start: 0.8378 (mmm) cc_final: 0.7986 (mmm) REVERT: B 154 TYR cc_start: 0.8120 (m-80) cc_final: 0.7748 (m-80) REVERT: B 212 ARG cc_start: 0.8251 (mtt90) cc_final: 0.8016 (mtt-85) REVERT: B 295 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8254 (mt-10) REVERT: B 315 MET cc_start: 0.8367 (tpp) cc_final: 0.8122 (tpp) REVERT: B 324 ASP cc_start: 0.7062 (m-30) cc_final: 0.6643 (m-30) REVERT: B 325 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7535 (mmmm) REVERT: B 339 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7385 (mtmm) REVERT: B 347 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 349 LYS cc_start: 0.8320 (mttt) cc_final: 0.7798 (mttt) REVERT: B 352 ASP cc_start: 0.6816 (t0) cc_final: 0.6052 (t0) REVERT: B 398 VAL cc_start: 0.8502 (t) cc_final: 0.8240 (p) REVERT: B 404 ARG cc_start: 0.7367 (mtm180) cc_final: 0.7088 (mtm180) REVERT: B 421 VAL cc_start: 0.7827 (t) cc_final: 0.7577 (t) REVERT: B 491 TYR cc_start: 0.7613 (t80) cc_final: 0.7331 (t80) REVERT: B 492 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7396 (mtm110) REVERT: B 520 TRP cc_start: 0.7855 (m100) cc_final: 0.7406 (m100) REVERT: C 51 THR cc_start: 0.8669 (t) cc_final: 0.8377 (p) REVERT: C 56 THR cc_start: 0.8313 (p) cc_final: 0.8020 (p) REVERT: C 101 THR cc_start: 0.8170 (t) cc_final: 0.7945 (m) REVERT: D 61 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7417 (mtpt) REVERT: D 169 MET cc_start: 0.8444 (ttp) cc_final: 0.8179 (tmm) REVERT: D 231 ILE cc_start: 0.8542 (mm) cc_final: 0.8267 (tt) REVERT: D 259 LEU cc_start: 0.8537 (mt) cc_final: 0.8308 (mp) REVERT: D 263 VAL cc_start: 0.8575 (t) cc_final: 0.8301 (p) REVERT: D 295 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 318 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7880 (ttpp) REVERT: D 324 ASP cc_start: 0.7746 (m-30) cc_final: 0.7108 (m-30) REVERT: D 395 ASN cc_start: 0.7262 (p0) cc_final: 0.6711 (p0) REVERT: D 423 LYS cc_start: 0.8385 (mttm) cc_final: 0.8062 (mtpp) REVERT: D 491 TYR cc_start: 0.7949 (t80) cc_final: 0.7626 (t80) REVERT: D 511 TYR cc_start: 0.8075 (p90) cc_final: 0.7313 (p90) outliers start: 11 outliers final: 8 residues processed: 235 average time/residue: 0.1110 time to fit residues: 35.5857 Evaluate side-chains 238 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 230 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER 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 C residue 102 THR 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: 0.9990 chunk 63 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 47 optimal weight: 0.0170 chunk 83 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103707 restraints weight = 24929.602| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.43 r_work: 0.3144 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11358 Z= 0.094 Angle : 0.470 10.905 15606 Z= 0.243 Chirality : 0.040 0.148 1740 Planarity : 0.004 0.039 1846 Dihedral : 11.686 73.914 2013 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 14.39 % 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: 0.24 (0.24), residues: 1275 helix: 1.15 (0.31), residues: 294 sheet: -0.94 (0.36), residues: 173 loop : 0.13 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.022 0.001 TYR D 447 PHE 0.021 0.001 PHE D 326 TRP 0.009 0.001 TRP B 385 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 (11317) covalent geometry : angle 0.46393 / 0.24 (15573) hydrogen bonds : bond 0.03408 / 2.27 ( 362) hydrogen bonds : angle 3.90622 / 2.68 ( 962) metal coordination : bond 0.00424 / 0.28 ( 40) metal coordination : angle 1.64188 / 1.11 ( 33) Misc. bond : bond 0.00058 / 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 245 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.244 Fit side-chains REVERT: A 5 THR cc_start: 0.8006 (m) cc_final: 0.7546 (m) REVERT: A 6 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7722 (tp30) REVERT: B 77 GLU cc_start: 0.7342 (mp0) cc_final: 0.7097 (mp0) REVERT: B 139 LYS cc_start: 0.8162 (tttt) cc_final: 0.7855 (ptmm) REVERT: B 153 MET cc_start: 0.8423 (mmm) cc_final: 0.8006 (mmm) REVERT: B 154 TYR cc_start: 0.8103 (m-80) cc_final: 0.7785 (m-80) REVERT: B 212 ARG cc_start: 0.8252 (mtt90) cc_final: 0.8018 (mtt-85) REVERT: B 295 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8283 (mt-10) REVERT: B 315 MET cc_start: 0.8386 (tpp) cc_final: 0.8140 (tpp) REVERT: B 324 ASP cc_start: 0.7148 (m-30) cc_final: 0.6724 (m-30) REVERT: B 325 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7556 (mmmm) REVERT: B 347 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 349 LYS cc_start: 0.8346 (mttt) cc_final: 0.7731 (mttt) REVERT: B 351 TYR cc_start: 0.8532 (m-80) cc_final: 0.7844 (m-80) REVERT: B 352 ASP cc_start: 0.6855 (t0) cc_final: 0.6257 (t0) REVERT: B 398 VAL cc_start: 0.8569 (t) cc_final: 0.8310 (p) REVERT: B 404 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7082 (mtm180) REVERT: B 421 VAL cc_start: 0.7812 (t) cc_final: 0.7570 (t) REVERT: B 491 TYR cc_start: 0.7600 (t80) cc_final: 0.7386 (t80) REVERT: B 492 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7410 (mtm110) REVERT: B 520 TRP cc_start: 0.7865 (m100) cc_final: 0.7416 (m100) REVERT: C 51 THR cc_start: 0.8654 (t) cc_final: 0.8382 (p) REVERT: C 56 THR cc_start: 0.8282 (p) cc_final: 0.7984 (p) REVERT: C 101 THR cc_start: 0.8150 (t) cc_final: 0.7940 (m) REVERT: D 35 THR cc_start: 0.7555 (m) cc_final: 0.7109 (p) REVERT: D 61 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7406 (mtpt) REVERT: D 169 MET cc_start: 0.8483 (ttp) cc_final: 0.8200 (tmm) REVERT: D 231 ILE cc_start: 0.8518 (mm) cc_final: 0.8224 (tt) REVERT: D 259 LEU cc_start: 0.8533 (mt) cc_final: 0.8289 (mp) REVERT: D 263 VAL cc_start: 0.8598 (t) cc_final: 0.8354 (p) REVERT: D 295 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8315 (mt-10) REVERT: D 318 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7813 (ttpt) REVERT: D 324 ASP cc_start: 0.7686 (m-30) cc_final: 0.7111 (m-30) REVERT: D 395 ASN cc_start: 0.7249 (p0) cc_final: 0.6597 (p0) REVERT: D 423 LYS cc_start: 0.8414 (mttm) cc_final: 0.8100 (mtpp) REVERT: D 491 TYR cc_start: 0.7934 (t80) cc_final: 0.7588 (t80) REVERT: D 511 TYR cc_start: 0.8154 (p90) cc_final: 0.7638 (p90) outliers start: 10 outliers final: 9 residues processed: 238 average time/residue: 0.1055 time to fit residues: 34.2411 Evaluate side-chains 239 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 129 SER 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 Chi-restraints excluded: chain D residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 306 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 = 0.3685 r_free = 0.3685 target = 0.132279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102941 restraints weight = 20791.737| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.18 r_work: 0.3139 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 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 = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11358 Z= 0.161 Angle : 0.502 11.230 15606 Z= 0.260 Chirality : 0.042 0.153 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.683 74.042 2013 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.00 % Allowed : 14.84 % Favored : 84.16 % 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: 0.20 (0.24), residues: 1275 helix: 1.10 (0.31), residues: 294 sheet: -1.02 (0.34), residues: 195 loop : 0.18 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 205 TYR 0.021 0.001 TYR D 447 PHE 0.023 0.002 PHE D 326 TRP 0.010 0.001 TRP B 520 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (11317) covalent geometry : angle 0.49529 / 0.26 (15573) hydrogen bonds : bond 0.03821 / 2.55 ( 362) hydrogen bonds : angle 3.99620 / 2.75 ( 962) metal coordination : bond 0.00849 / 0.59 ( 40) metal coordination : angle 1.82396 / 1.22 ( 33) Misc. bond : bond 0.00017 / 0.01 ( 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 242 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 0.314 Fit side-chains REVERT: A 5 THR cc_start: 0.8039 (m) cc_final: 0.7551 (m) REVERT: A 6 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7705 (tp30) REVERT: B 77 GLU cc_start: 0.7315 (mp0) cc_final: 0.7069 (mp0) REVERT: B 139 LYS cc_start: 0.8138 (tttt) cc_final: 0.7877 (ptmm) REVERT: B 154 TYR cc_start: 0.8114 (m-80) cc_final: 0.7760 (m-80) REVERT: B 212 ARG cc_start: 0.8268 (mtt90) cc_final: 0.8038 (mtt-85) REVERT: B 295 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 315 MET cc_start: 0.8374 (tpp) cc_final: 0.8125 (tpp) REVERT: B 324 ASP cc_start: 0.7081 (m-30) cc_final: 0.6666 (m-30) REVERT: B 325 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7549 (mmmm) REVERT: B 347 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 349 LYS cc_start: 0.8356 (mttt) cc_final: 0.7746 (mttt) REVERT: B 351 TYR cc_start: 0.8544 (m-80) cc_final: 0.7942 (m-80) REVERT: B 352 ASP cc_start: 0.6847 (t0) cc_final: 0.6251 (t0) REVERT: B 398 VAL cc_start: 0.8531 (t) cc_final: 0.8268 (p) REVERT: B 404 ARG cc_start: 0.7359 (mtm180) cc_final: 0.7011 (mtm180) REVERT: B 421 VAL cc_start: 0.7811 (t) cc_final: 0.7553 (t) REVERT: B 491 TYR cc_start: 0.7606 (t80) cc_final: 0.7309 (t80) REVERT: B 492 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7411 (mtm110) REVERT: B 520 TRP cc_start: 0.7897 (m100) cc_final: 0.7482 (m100) REVERT: C 51 THR cc_start: 0.8662 (t) cc_final: 0.8379 (p) REVERT: C 56 THR cc_start: 0.8286 (p) cc_final: 0.7999 (p) REVERT: C 101 THR cc_start: 0.8176 (t) cc_final: 0.7958 (m) REVERT: D 61 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7430 (mtpt) REVERT: D 169 MET cc_start: 0.8465 (ttp) cc_final: 0.8188 (tmm) REVERT: D 231 ILE cc_start: 0.8548 (mm) cc_final: 0.8268 (tt) REVERT: D 259 LEU cc_start: 0.8516 (mt) cc_final: 0.8292 (mp) REVERT: D 263 VAL cc_start: 0.8595 (t) cc_final: 0.8330 (p) REVERT: D 295 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 318 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7834 (ttpt) REVERT: D 324 ASP cc_start: 0.7625 (m-30) cc_final: 0.7233 (m-30) REVERT: D 395 ASN cc_start: 0.7259 (p0) cc_final: 0.6627 (p0) REVERT: D 423 LYS cc_start: 0.8433 (mttm) cc_final: 0.8105 (mtpp) REVERT: D 444 PHE cc_start: 0.7919 (t80) cc_final: 0.7698 (t80) REVERT: D 491 TYR cc_start: 0.7961 (t80) cc_final: 0.7673 (t80) REVERT: D 511 TYR cc_start: 0.8032 (p90) cc_final: 0.7432 (p90) outliers start: 11 outliers final: 10 residues processed: 234 average time/residue: 0.1044 time to fit residues: 33.2008 Evaluate side-chains 240 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER 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 C residue 102 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 477 CYS Chi-restraints excluded: chain D residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9980 chunk 121 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102113 restraints weight = 26188.277| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.55 r_work: 0.3111 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 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: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11358 Z= 0.135 Angle : 0.488 11.037 15606 Z= 0.253 Chirality : 0.041 0.153 1740 Planarity : 0.004 0.041 1846 Dihedral : 11.664 73.961 2013 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 14.57 % Favored : 84.52 % 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: 0.21 (0.24), residues: 1275 helix: 1.10 (0.31), residues: 294 sheet: -1.00 (0.34), residues: 195 loop : 0.18 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 205 TYR 0.022 0.001 TYR D 447 PHE 0.020 0.001 PHE D 326 TRP 0.009 0.001 TRP B 385 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (11317) covalent geometry : angle 0.48133 / 0.25 (15573) hydrogen bonds : bond 0.03683 / 2.45 ( 362) hydrogen bonds : angle 3.98170 / 2.74 ( 962) metal coordination : bond 0.00649 / 0.45 ( 40) metal coordination : angle 1.76897 / 1.18 ( 33) Misc. bond : bond 0.00034 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.10 seconds wall clock time: 62 minutes 33.96 seconds (3753.96 seconds total)