Starting phenix.real_space_refine on Sun May 3 06:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrk_73369/05_2026/9yrk_73369.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 1.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 10 6.06 5 P 40 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 6820 2.51 5 N 1861 2.21 5 O 2113 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 3.63, per 1000 atoms: 0.33 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: 0.85 Conformation dependent library (CDL) restraints added in 708.2 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: 1.28 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: 1.82 Time building geometry restraints manager: 1.06 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: 3.090 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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= 0.195 Angle : 0.600 12.695 15606 Z= 0.321 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 covalent geometry : bond 0.00410 (11317) covalent geometry : angle 0.59442 (15573) hydrogen bonds : bond 0.14426 ( 362) hydrogen bonds : angle 5.95311 ( 962) metal coordination : bond 0.00752 ( 40) metal coordination : angle 1.94476 ( 33) Misc. bond : bond 0.04112 ( 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 : 0.357 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: 0.1353 time to fit residues: 51.0813 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 : 0.391 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3679 r_free = 0.3679 target = 0.131778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102172 restraints weight = 21786.233| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.27 r_work: 0.3120 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11358 Z= 0.151 Angle : 0.511 5.368 15606 Z= 0.265 Chirality : 0.042 0.158 1740 Planarity : 0.004 0.045 1846 Dihedral : 11.924 73.954 2013 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.90 % Allowed : 10.68 % Favored : 88.42 % 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: -0.01 (0.24), residues: 1275 helix: 0.66 (0.31), residues: 294 sheet: -1.08 (0.36), residues: 173 loop : 0.10 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.017 0.001 TYR B 420 PHE 0.031 0.002 PHE B 350 TRP 0.013 0.001 TRP B 348 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00354 (11317) covalent geometry : angle 0.50227 (15573) hydrogen bonds : bond 0.04207 ( 362) hydrogen bonds : angle 4.42712 ( 962) metal coordination : bond 0.00939 ( 40) metal coordination : angle 2.08186 ( 33) Misc. bond : bond 0.00018 ( 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 264 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7514 (tp30) REVERT: A 56 THR cc_start: 0.8309 (p) cc_final: 0.8078 (p) REVERT: A 58 THR cc_start: 0.8443 (t) cc_final: 0.8055 (t) REVERT: A 122 MET cc_start: 0.8579 (mmt) cc_final: 0.8113 (mmm) REVERT: B 13 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7761 (mtmt) REVERT: B 30 ASP cc_start: 0.7775 (t0) cc_final: 0.7487 (t0) REVERT: B 71 ASN cc_start: 0.7833 (m110) cc_final: 0.7630 (t0) REVERT: B 77 GLU cc_start: 0.7427 (mp0) cc_final: 0.7186 (mp0) REVERT: B 92 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 98 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7878 (mtm110) REVERT: B 139 LYS cc_start: 0.8137 (tttt) cc_final: 0.7862 (ptmm) REVERT: B 153 MET cc_start: 0.8474 (mmm) cc_final: 0.8224 (mmm) REVERT: B 154 TYR cc_start: 0.8211 (m-80) cc_final: 0.7873 (m-80) REVERT: B 195 MET cc_start: 0.8263 (mtt) cc_final: 0.8020 (mtt) REVERT: B 212 ARG cc_start: 0.8306 (mtt90) cc_final: 0.8093 (mtt-85) REVERT: B 284 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 304 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7913 (mmtt) REVERT: B 315 MET cc_start: 0.8362 (tpp) cc_final: 0.8120 (tpp) REVERT: B 324 ASP cc_start: 0.7158 (m-30) cc_final: 0.6644 (m-30) REVERT: B 339 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7285 (mtmm) REVERT: B 347 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 349 LYS cc_start: 0.8290 (mttt) cc_final: 0.7792 (mttt) REVERT: B 352 ASP cc_start: 0.6808 (t0) cc_final: 0.6078 (t0) REVERT: B 398 VAL cc_start: 0.8528 (t) cc_final: 0.8264 (p) REVERT: B 404 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7190 (mtm180) REVERT: B 421 VAL cc_start: 0.7787 (t) cc_final: 0.7537 (t) REVERT: B 491 TYR cc_start: 0.7642 (t80) cc_final: 0.7343 (t80) REVERT: B 492 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7470 (mtm110) REVERT: C 6 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 51 THR cc_start: 0.8624 (t) cc_final: 0.8376 (p) REVERT: C 56 THR cc_start: 0.8372 (p) cc_final: 0.8092 (p) REVERT: D 61 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7461 (mtpt) REVERT: D 169 MET cc_start: 0.8428 (ttp) cc_final: 0.8187 (tmm) REVERT: D 211 ASP cc_start: 0.7821 (t0) cc_final: 0.7457 (t0) REVERT: D 231 ILE cc_start: 0.8548 (mm) cc_final: 0.8286 (tt) REVERT: D 246 GLN cc_start: 0.8171 (mt0) cc_final: 0.7831 (mt0) REVERT: D 259 LEU cc_start: 0.8592 (mt) cc_final: 0.8327 (mp) REVERT: D 263 VAL cc_start: 0.8588 (t) cc_final: 0.8304 (p) REVERT: D 295 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 310 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7699 (mtp180) REVERT: D 311 LYS cc_start: 0.8416 (tttt) cc_final: 0.7860 (ttmm) REVERT: D 318 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7839 (ttpt) REVERT: D 324 ASP cc_start: 0.7812 (m-30) cc_final: 0.7163 (m-30) REVERT: D 326 PHE cc_start: 0.8308 (m-80) cc_final: 0.7967 (m-10) REVERT: D 331 ASP cc_start: 0.7637 (t0) cc_final: 0.7142 (t0) REVERT: D 423 LYS cc_start: 0.8399 (mttm) cc_final: 0.8092 (mtpp) REVERT: D 491 TYR cc_start: 0.7964 (t80) cc_final: 0.7710 (t80) outliers start: 10 outliers final: 3 residues processed: 261 average time/residue: 0.1313 time to fit residues: 45.4150 Evaluate side-chains 250 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 83 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 HIS C 40 ASN C 98 GLN D 108 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 = 0.131853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101845 restraints weight = 24655.300| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.43 r_work: 0.3110 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11358 Z= 0.145 Angle : 0.503 6.889 15606 Z= 0.258 Chirality : 0.041 0.157 1740 Planarity : 0.004 0.044 1846 Dihedral : 11.869 73.974 2013 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.81 % Allowed : 12.67 % 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: 0.87 (0.31), residues: 294 sheet: -1.09 (0.35), residues: 185 loop : 0.16 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.017 0.001 TYR B 420 PHE 0.015 0.001 PHE B 444 TRP 0.017 0.001 TRP B 348 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00344 (11317) covalent geometry : angle 0.49548 (15573) hydrogen bonds : bond 0.03870 ( 362) hydrogen bonds : angle 4.22686 ( 962) metal coordination : bond 0.00750 ( 40) metal coordination : angle 1.94416 ( 33) Misc. bond : bond 0.00006 ( 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 261 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7646 (tp30) REVERT: A 58 THR cc_start: 0.8427 (t) cc_final: 0.8016 (t) REVERT: B 13 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7794 (mtmt) REVERT: B 71 ASN cc_start: 0.7803 (m110) cc_final: 0.7597 (t0) REVERT: B 77 GLU cc_start: 0.7446 (mp0) cc_final: 0.7205 (mp0) REVERT: B 92 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 98 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7913 (mtm110) REVERT: B 122 THR cc_start: 0.8265 (m) cc_final: 0.8037 (p) REVERT: B 139 LYS cc_start: 0.8159 (tttt) cc_final: 0.7880 (ptmm) REVERT: B 153 MET cc_start: 0.8469 (mmm) cc_final: 0.8254 (mmm) REVERT: B 154 TYR cc_start: 0.8201 (m-80) cc_final: 0.7818 (m-80) REVERT: B 212 ARG cc_start: 0.8304 (mtt90) cc_final: 0.8083 (mtt-85) REVERT: B 304 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7932 (mmtt) REVERT: B 315 MET cc_start: 0.8397 (tpp) cc_final: 0.8166 (tpp) REVERT: B 324 ASP cc_start: 0.7164 (m-30) cc_final: 0.6661 (m-30) REVERT: B 339 LYS cc_start: 0.7627 (mtmm) cc_final: 0.7357 (mtmm) REVERT: B 347 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7228 (mm-30) REVERT: B 349 LYS cc_start: 0.8363 (mttt) cc_final: 0.7709 (mttt) REVERT: B 351 TYR cc_start: 0.8530 (m-80) cc_final: 0.7899 (m-80) REVERT: B 352 ASP cc_start: 0.6877 (t0) cc_final: 0.6149 (t0) REVERT: B 398 VAL cc_start: 0.8568 (t) cc_final: 0.8319 (p) REVERT: B 404 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7228 (mtm180) REVERT: B 421 VAL cc_start: 0.7842 (t) cc_final: 0.7581 (t) REVERT: B 491 TYR cc_start: 0.7694 (t80) cc_final: 0.7402 (t80) REVERT: B 492 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7464 (mtm110) REVERT: C 6 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 51 THR cc_start: 0.8636 (t) cc_final: 0.8381 (p) REVERT: C 56 THR cc_start: 0.8382 (p) cc_final: 0.8094 (p) REVERT: D 35 THR cc_start: 0.7561 (m) cc_final: 0.7038 (p) REVERT: D 61 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7422 (mtpt) REVERT: D 211 ASP cc_start: 0.7866 (t0) cc_final: 0.7529 (t0) REVERT: D 231 ILE cc_start: 0.8569 (mm) cc_final: 0.8301 (tt) REVERT: D 246 GLN cc_start: 0.8205 (mt0) cc_final: 0.7908 (mt0) REVERT: D 259 LEU cc_start: 0.8590 (mt) cc_final: 0.8339 (mp) REVERT: D 263 VAL cc_start: 0.8598 (t) cc_final: 0.8305 (p) REVERT: D 295 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8339 (mt-10) REVERT: D 310 ARG cc_start: 0.8011 (mtp180) cc_final: 0.7708 (mtp180) REVERT: D 311 LYS cc_start: 0.8433 (tttt) cc_final: 0.8178 (ttmm) REVERT: D 318 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7895 (ttpt) REVERT: D 324 ASP cc_start: 0.7778 (m-30) cc_final: 0.7079 (m-30) REVERT: D 326 PHE cc_start: 0.8323 (m-80) cc_final: 0.7956 (m-10) REVERT: D 395 ASN cc_start: 0.7446 (p0) cc_final: 0.6994 (p0) REVERT: D 423 LYS cc_start: 0.8433 (mttm) cc_final: 0.8121 (mtpp) REVERT: D 491 TYR cc_start: 0.7992 (t80) cc_final: 0.7685 (t80) outliers start: 9 outliers final: 5 residues processed: 255 average time/residue: 0.1339 time to fit residues: 44.7588 Evaluate side-chains 249 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 244 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 254 GLN B 314 HIS C 40 ASN C 98 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 = 0.3682 r_free = 0.3682 target = 0.132101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101832 restraints weight = 26135.950| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.54 r_work: 0.3108 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11358 Z= 0.126 Angle : 0.484 6.420 15606 Z= 0.249 Chirality : 0.041 0.156 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.797 73.920 2013 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.18 % Allowed : 13.03 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1275 helix: 0.97 (0.31), residues: 294 sheet: -1.07 (0.35), residues: 185 loop : 0.16 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.017 0.001 TYR D 447 PHE 0.015 0.001 PHE D 444 TRP 0.011 0.001 TRP B 348 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00297 (11317) covalent geometry : angle 0.47723 (15573) hydrogen bonds : bond 0.03596 ( 362) hydrogen bonds : angle 4.09268 ( 962) metal coordination : bond 0.00653 ( 40) metal coordination : angle 1.79572 ( 33) Misc. bond : bond 0.00007 ( 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 259 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7698 (tp30) REVERT: B 13 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7748 (mtmt) REVERT: B 65 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7501 (tm-30) REVERT: B 77 GLU cc_start: 0.7455 (mp0) cc_final: 0.7204 (mp0) REVERT: B 98 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7968 (mtm110) REVERT: B 122 THR cc_start: 0.8264 (m) cc_final: 0.8041 (p) REVERT: B 139 LYS cc_start: 0.8189 (tttt) cc_final: 0.7909 (ptmm) REVERT: B 153 MET cc_start: 0.8451 (mmm) cc_final: 0.8033 (mmm) REVERT: B 154 TYR cc_start: 0.8164 (m-80) cc_final: 0.7795 (m-80) REVERT: B 212 ARG cc_start: 0.8300 (mtt90) cc_final: 0.8077 (mtt-85) REVERT: B 304 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7924 (mmtt) REVERT: B 315 MET cc_start: 0.8404 (tpp) cc_final: 0.8176 (tpp) REVERT: B 324 ASP cc_start: 0.7148 (m-30) cc_final: 0.6644 (m-30) REVERT: B 339 LYS cc_start: 0.7637 (mtmm) cc_final: 0.7391 (mtmm) REVERT: B 347 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7236 (mm-30) REVERT: B 349 LYS cc_start: 0.8382 (mttt) cc_final: 0.7854 (mttt) REVERT: B 352 ASP cc_start: 0.6855 (t0) cc_final: 0.6117 (t0) REVERT: B 398 VAL cc_start: 0.8574 (t) cc_final: 0.8319 (p) REVERT: B 404 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7249 (mtm180) REVERT: B 421 VAL cc_start: 0.7855 (t) cc_final: 0.7598 (t) REVERT: B 491 TYR cc_start: 0.7695 (t80) cc_final: 0.7356 (t80) REVERT: B 492 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7450 (mtm110) REVERT: C 51 THR cc_start: 0.8651 (t) cc_final: 0.8383 (p) REVERT: C 56 THR cc_start: 0.8343 (p) cc_final: 0.8045 (p) REVERT: C 101 THR cc_start: 0.8186 (t) cc_final: 0.7962 (m) REVERT: D 35 THR cc_start: 0.7561 (m) cc_final: 0.7062 (p) REVERT: D 61 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7437 (mtpt) REVERT: D 211 ASP cc_start: 0.7871 (t0) cc_final: 0.7439 (t0) REVERT: D 231 ILE cc_start: 0.8565 (mm) cc_final: 0.8289 (tt) REVERT: D 246 GLN cc_start: 0.8180 (mt0) cc_final: 0.7950 (mt0) REVERT: D 259 LEU cc_start: 0.8585 (mt) cc_final: 0.8346 (mp) REVERT: D 263 VAL cc_start: 0.8602 (t) cc_final: 0.8325 (p) REVERT: D 295 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 318 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7873 (ttpt) REVERT: D 324 ASP cc_start: 0.7702 (m-30) cc_final: 0.6994 (m-30) REVERT: D 326 PHE cc_start: 0.8332 (m-80) cc_final: 0.7964 (m-10) REVERT: D 395 ASN cc_start: 0.7458 (p0) cc_final: 0.6994 (p0) REVERT: D 423 LYS cc_start: 0.8453 (mttm) cc_final: 0.8141 (mtpp) REVERT: D 491 TYR cc_start: 0.7993 (t80) cc_final: 0.7619 (t80) outliers start: 13 outliers final: 11 residues processed: 251 average time/residue: 0.1267 time to fit residues: 42.4705 Evaluate side-chains 254 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 215 THR 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 309 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 51 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3687 r_free = 0.3687 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102449 restraints weight = 23551.564| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.39 r_work: 0.3124 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 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 = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11358 Z= 0.130 Angle : 0.479 7.040 15606 Z= 0.247 Chirality : 0.041 0.151 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.749 73.926 2013 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 13.39 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1275 helix: 1.04 (0.31), residues: 294 sheet: -1.05 (0.35), residues: 185 loop : 0.22 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.018 0.001 TYR D 447 PHE 0.018 0.001 PHE D 444 TRP 0.009 0.001 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00308 (11317) covalent geometry : angle 0.47272 (15573) hydrogen bonds : bond 0.03548 ( 362) hydrogen bonds : angle 4.05819 ( 962) metal coordination : bond 0.00653 ( 40) metal coordination : angle 1.77768 ( 33) Misc. bond : bond 0.00009 ( 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 259 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.391 Fit side-chains REVERT: A 5 THR cc_start: 0.8053 (m) cc_final: 0.7603 (m) REVERT: A 6 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7727 (tp30) REVERT: B 13 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7761 (mtmt) REVERT: B 65 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7485 (tm-30) REVERT: B 77 GLU cc_start: 0.7439 (mp0) cc_final: 0.7193 (mp0) REVERT: B 98 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7958 (mtm110) REVERT: B 122 THR cc_start: 0.8273 (m) cc_final: 0.8041 (p) REVERT: B 139 LYS cc_start: 0.8197 (tttt) cc_final: 0.7923 (ptmm) REVERT: B 153 MET cc_start: 0.8424 (mmm) cc_final: 0.8060 (mmm) REVERT: B 154 TYR cc_start: 0.8156 (m-80) cc_final: 0.7796 (m-80) REVERT: B 212 ARG cc_start: 0.8285 (mtt90) cc_final: 0.8071 (mtt-85) REVERT: B 227 TRP cc_start: 0.8653 (m100) cc_final: 0.8104 (m100) REVERT: B 295 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 304 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7914 (mmtt) REVERT: B 310 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8168 (mtp180) REVERT: B 315 MET cc_start: 0.8396 (tpp) cc_final: 0.8167 (tpp) REVERT: B 324 ASP cc_start: 0.7110 (m-30) cc_final: 0.6730 (m-30) REVERT: B 339 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7392 (mtmm) REVERT: B 347 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 349 LYS cc_start: 0.8351 (mttt) cc_final: 0.7858 (mttt) REVERT: B 352 ASP cc_start: 0.6887 (t0) cc_final: 0.6130 (t0) REVERT: B 398 VAL cc_start: 0.8559 (t) cc_final: 0.8307 (p) REVERT: B 404 ARG cc_start: 0.7496 (mtm180) cc_final: 0.7252 (mtm180) REVERT: B 421 VAL cc_start: 0.7849 (t) cc_final: 0.7594 (t) REVERT: B 491 TYR cc_start: 0.7707 (t80) cc_final: 0.7410 (t80) REVERT: B 492 ARG cc_start: 0.7833 (mtm180) cc_final: 0.7468 (mtm110) REVERT: B 520 TRP cc_start: 0.7910 (m100) cc_final: 0.7433 (m100) REVERT: C 40 ASN cc_start: 0.8868 (t0) cc_final: 0.8622 (t0) REVERT: C 51 THR cc_start: 0.8668 (t) cc_final: 0.8389 (p) REVERT: C 56 THR cc_start: 0.8285 (p) cc_final: 0.7998 (p) REVERT: C 101 THR cc_start: 0.8187 (t) cc_final: 0.7958 (m) REVERT: D 35 THR cc_start: 0.7581 (m) cc_final: 0.7108 (p) REVERT: D 61 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7413 (mtpt) REVERT: D 62 MET cc_start: 0.8543 (mmm) cc_final: 0.8306 (mmm) REVERT: D 169 MET cc_start: 0.8503 (ttp) cc_final: 0.8252 (tmm) REVERT: D 211 ASP cc_start: 0.7864 (t0) cc_final: 0.7506 (t0) REVERT: D 231 ILE cc_start: 0.8568 (mm) cc_final: 0.8292 (tt) REVERT: D 246 GLN cc_start: 0.8151 (mt0) cc_final: 0.7929 (mt0) REVERT: D 259 LEU cc_start: 0.8568 (mt) cc_final: 0.8341 (mp) REVERT: D 263 VAL cc_start: 0.8605 (t) cc_final: 0.8332 (p) REVERT: D 295 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8319 (mt-10) REVERT: D 310 ARG cc_start: 0.8006 (mtp180) cc_final: 0.7720 (mtp180) REVERT: D 318 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7890 (ttpt) REVERT: D 324 ASP cc_start: 0.7654 (m-30) cc_final: 0.6565 (m-30) REVERT: D 326 PHE cc_start: 0.8321 (m-80) cc_final: 0.7998 (m-10) REVERT: D 395 ASN cc_start: 0.7431 (p0) cc_final: 0.6974 (p0) REVERT: D 423 LYS cc_start: 0.8453 (mttm) cc_final: 0.8144 (mtpp) REVERT: D 491 TYR cc_start: 0.7992 (t80) cc_final: 0.7586 (t80) REVERT: D 501 MET cc_start: 0.7677 (ttp) cc_final: 0.7320 (ttt) REVERT: D 511 TYR cc_start: 0.8039 (p90) cc_final: 0.7260 (p90) outliers start: 10 outliers final: 8 residues processed: 253 average time/residue: 0.1241 time to fit residues: 41.9500 Evaluate side-chains 254 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 246 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 16 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 254 GLN B 314 HIS C 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101315 restraints weight = 25877.913| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.52 r_work: 0.3099 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11358 Z= 0.170 Angle : 0.501 6.537 15606 Z= 0.258 Chirality : 0.042 0.146 1740 Planarity : 0.004 0.043 1846 Dihedral : 11.730 74.060 2013 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.36 % Allowed : 13.76 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1275 helix: 1.04 (0.31), residues: 294 sheet: -0.98 (0.35), 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 0.019 0.001 TYR D 447 PHE 0.024 0.002 PHE D 444 TRP 0.009 0.001 TRP B 520 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00410 (11317) covalent geometry : angle 0.49407 (15573) hydrogen bonds : bond 0.03783 ( 362) hydrogen bonds : angle 4.09904 ( 962) metal coordination : bond 0.00840 ( 40) metal coordination : angle 1.92963 ( 33) Misc. bond : bond 0.00024 ( 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 259 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8088 (m) cc_final: 0.7620 (m) REVERT: A 6 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7718 (tp30) REVERT: B 13 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7739 (mtmt) REVERT: B 65 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7530 (tm-30) REVERT: B 77 GLU cc_start: 0.7474 (mp0) cc_final: 0.7221 (mp0) REVERT: B 98 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7961 (mtm110) REVERT: B 122 THR cc_start: 0.8283 (m) cc_final: 0.8011 (p) REVERT: B 139 LYS cc_start: 0.8190 (tttt) cc_final: 0.7908 (ptmm) REVERT: B 153 MET cc_start: 0.8399 (mmm) cc_final: 0.8021 (mmm) REVERT: B 154 TYR cc_start: 0.8175 (m-80) cc_final: 0.7824 (m-80) REVERT: B 212 ARG cc_start: 0.8310 (mtt90) cc_final: 0.8084 (mtt-85) REVERT: B 295 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8316 (mt-10) REVERT: B 304 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7935 (mmtt) REVERT: B 310 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8178 (mtp180) REVERT: B 315 MET cc_start: 0.8417 (tpp) cc_final: 0.8183 (tpp) REVERT: B 324 ASP cc_start: 0.7294 (m-30) cc_final: 0.6847 (m-30) REVERT: B 339 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7432 (mtmm) REVERT: B 347 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 349 LYS cc_start: 0.8382 (mttt) cc_final: 0.8021 (mttt) REVERT: B 352 ASP cc_start: 0.6921 (t0) cc_final: 0.6140 (t0) REVERT: B 398 VAL cc_start: 0.8559 (t) cc_final: 0.8309 (p) REVERT: B 404 ARG cc_start: 0.7502 (mtm180) cc_final: 0.7276 (mtm180) REVERT: B 421 VAL cc_start: 0.7869 (t) cc_final: 0.7612 (t) REVERT: B 491 TYR cc_start: 0.7727 (t80) cc_final: 0.7400 (t80) REVERT: B 492 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7512 (mtm110) REVERT: B 520 TRP cc_start: 0.7949 (m100) cc_final: 0.7506 (m100) REVERT: C 51 THR cc_start: 0.8679 (t) cc_final: 0.8398 (p) REVERT: C 56 THR cc_start: 0.8304 (p) cc_final: 0.8007 (p) REVERT: C 101 THR cc_start: 0.8200 (t) cc_final: 0.7976 (m) REVERT: D 61 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7404 (mtpt) REVERT: D 62 MET cc_start: 0.8566 (mmm) cc_final: 0.8341 (mmm) REVERT: D 169 MET cc_start: 0.8513 (ttp) cc_final: 0.8247 (tmm) REVERT: D 211 ASP cc_start: 0.7865 (t0) cc_final: 0.7517 (t0) REVERT: D 231 ILE cc_start: 0.8564 (mm) cc_final: 0.8297 (tt) REVERT: D 259 LEU cc_start: 0.8610 (mt) cc_final: 0.8375 (mp) REVERT: D 263 VAL cc_start: 0.8592 (t) cc_final: 0.8320 (p) REVERT: D 295 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8357 (mt-10) REVERT: D 318 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7882 (ttpt) REVERT: D 324 ASP cc_start: 0.7707 (m-30) cc_final: 0.6813 (m-30) REVERT: D 326 PHE cc_start: 0.8358 (m-80) cc_final: 0.8058 (m-10) REVERT: D 395 ASN cc_start: 0.7422 (p0) cc_final: 0.6951 (p0) REVERT: D 423 LYS cc_start: 0.8470 (mttm) cc_final: 0.8150 (mtpp) REVERT: D 491 TYR cc_start: 0.7989 (t80) cc_final: 0.7673 (t80) REVERT: D 501 MET cc_start: 0.7664 (ttp) cc_final: 0.7346 (ttm) REVERT: D 511 TYR cc_start: 0.7958 (p90) cc_final: 0.7249 (p90) REVERT: D 515 ASP cc_start: 0.6773 (t0) cc_final: 0.6456 (t0) outliers start: 15 outliers final: 13 residues processed: 250 average time/residue: 0.1277 time to fit residues: 42.4799 Evaluate side-chains 255 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 C residue 102 THR Chi-restraints excluded: chain D residue 29 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 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 = 0.3689 r_free = 0.3689 target = 0.132523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102424 restraints weight = 24830.924| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.46 r_work: 0.3121 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11358 Z= 0.117 Angle : 0.483 10.134 15606 Z= 0.247 Chirality : 0.041 0.149 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.677 73.919 2013 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.09 % Allowed : 14.30 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1275 helix: 1.11 (0.31), residues: 294 sheet: -1.05 (0.35), residues: 185 loop : 0.20 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.020 0.001 TYR D 447 PHE 0.028 0.001 PHE D 444 TRP 0.009 0.001 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00275 (11317) covalent geometry : angle 0.47690 (15573) hydrogen bonds : bond 0.03442 ( 362) hydrogen bonds : angle 3.98630 ( 962) metal coordination : bond 0.00547 ( 40) metal coordination : angle 1.71506 ( 33) Misc. bond : bond 0.00046 ( 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 249 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8053 (m) cc_final: 0.7571 (m) REVERT: A 6 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7726 (tp30) REVERT: B 65 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7531 (tm-30) REVERT: B 77 GLU cc_start: 0.7384 (mp0) cc_final: 0.7135 (mp0) REVERT: B 122 THR cc_start: 0.8268 (m) cc_final: 0.8026 (p) REVERT: B 139 LYS cc_start: 0.8175 (tttt) cc_final: 0.7879 (ptmm) REVERT: B 153 MET cc_start: 0.8409 (mmm) cc_final: 0.8007 (mmm) REVERT: B 154 TYR cc_start: 0.8153 (m-80) cc_final: 0.7793 (m-80) REVERT: B 212 ARG cc_start: 0.8275 (mtt90) cc_final: 0.8045 (mtt-85) REVERT: B 295 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 304 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7913 (mmtt) REVERT: B 310 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8145 (mtp180) REVERT: B 315 MET cc_start: 0.8399 (tpp) cc_final: 0.8146 (tpp) REVERT: B 324 ASP cc_start: 0.7357 (m-30) cc_final: 0.6761 (m-30) REVERT: B 325 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7444 (mmmm) REVERT: B 339 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7402 (mtmm) REVERT: B 347 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 349 LYS cc_start: 0.8357 (mttt) cc_final: 0.7995 (mttt) REVERT: B 352 ASP cc_start: 0.6864 (t0) cc_final: 0.6081 (t0) REVERT: B 398 VAL cc_start: 0.8546 (t) cc_final: 0.8288 (p) REVERT: B 404 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7237 (mtm180) REVERT: B 421 VAL cc_start: 0.7858 (t) cc_final: 0.7609 (t) REVERT: B 491 TYR cc_start: 0.7642 (t80) cc_final: 0.7354 (t80) REVERT: B 492 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7446 (mtm110) REVERT: B 520 TRP cc_start: 0.7920 (m100) cc_final: 0.7490 (m100) REVERT: C 40 ASN cc_start: 0.8864 (t0) cc_final: 0.8646 (t0) REVERT: C 51 THR cc_start: 0.8665 (t) cc_final: 0.8389 (p) REVERT: C 56 THR cc_start: 0.8286 (p) cc_final: 0.7994 (p) REVERT: C 101 THR cc_start: 0.8175 (t) cc_final: 0.7955 (m) REVERT: D 35 THR cc_start: 0.7564 (m) cc_final: 0.7098 (p) REVERT: D 61 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7372 (mtpt) REVERT: D 169 MET cc_start: 0.8493 (ttp) cc_final: 0.8223 (tmm) REVERT: D 211 ASP cc_start: 0.7834 (t0) cc_final: 0.7437 (t0) REVERT: D 231 ILE cc_start: 0.8547 (mm) cc_final: 0.8271 (tt) REVERT: D 259 LEU cc_start: 0.8544 (mt) cc_final: 0.8313 (mp) REVERT: D 263 VAL cc_start: 0.8583 (t) cc_final: 0.8311 (p) REVERT: D 295 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8332 (mt-10) REVERT: D 318 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7862 (ttpt) REVERT: D 324 ASP cc_start: 0.7645 (m-30) cc_final: 0.6674 (m-30) REVERT: D 326 PHE cc_start: 0.8333 (m-80) cc_final: 0.7997 (m-10) REVERT: D 395 ASN cc_start: 0.7444 (p0) cc_final: 0.6996 (p0) REVERT: D 423 LYS cc_start: 0.8451 (mttm) cc_final: 0.8125 (mtpp) REVERT: D 491 TYR cc_start: 0.7965 (t80) cc_final: 0.7596 (t80) REVERT: D 501 MET cc_start: 0.7636 (ttp) cc_final: 0.7320 (ttm) REVERT: D 511 TYR cc_start: 0.7919 (p90) cc_final: 0.7196 (p90) REVERT: D 515 ASP cc_start: 0.6712 (t0) cc_final: 0.6420 (t0) outliers start: 12 outliers final: 11 residues processed: 242 average time/residue: 0.1260 time to fit residues: 40.9322 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 : 0.358 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 341 VAL 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: 0.0980 chunk 21 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104019 restraints weight = 21059.919| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.24 r_work: 0.3156 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11358 Z= 0.098 Angle : 0.472 9.846 15606 Z= 0.241 Chirality : 0.040 0.148 1740 Planarity : 0.004 0.041 1846 Dihedral : 11.617 73.893 2013 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.09 % Allowed : 14.30 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1275 helix: 1.21 (0.31), residues: 294 sheet: -1.03 (0.36), residues: 173 loop : 0.15 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 205 TYR 0.020 0.001 TYR D 447 PHE 0.013 0.001 PHE D 444 TRP 0.009 0.001 TRP B 385 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00226 (11317) covalent geometry : angle 0.46682 (15573) hydrogen bonds : bond 0.03196 ( 362) hydrogen bonds : angle 3.85689 ( 962) metal coordination : bond 0.00452 ( 40) metal coordination : angle 1.60429 ( 33) Misc. bond : bond 0.00055 ( 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 240 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.394 Fit side-chains REVERT: A 5 THR cc_start: 0.8042 (m) cc_final: 0.7575 (m) REVERT: A 6 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7682 (tp30) REVERT: B 65 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7484 (tm-30) REVERT: B 77 GLU cc_start: 0.7314 (mp0) cc_final: 0.7059 (mp0) REVERT: B 122 THR cc_start: 0.8249 (m) cc_final: 0.8032 (p) REVERT: B 139 LYS cc_start: 0.8162 (tttt) cc_final: 0.7879 (ptmm) REVERT: B 153 MET cc_start: 0.8422 (mmm) cc_final: 0.8012 (mmm) REVERT: B 154 TYR cc_start: 0.8118 (m-80) cc_final: 0.7800 (m-80) REVERT: B 212 ARG cc_start: 0.8247 (mtt90) cc_final: 0.8014 (mtt-85) REVERT: B 295 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 310 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8075 (mtp180) REVERT: B 315 MET cc_start: 0.8356 (tpp) cc_final: 0.8099 (tpp) REVERT: B 324 ASP cc_start: 0.7321 (m-30) cc_final: 0.6739 (m-30) REVERT: B 325 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7456 (mmmm) REVERT: B 347 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 349 LYS cc_start: 0.8338 (mttt) cc_final: 0.7757 (mttt) REVERT: B 351 TYR cc_start: 0.8534 (m-80) cc_final: 0.7915 (m-80) REVERT: B 352 ASP cc_start: 0.6864 (t0) cc_final: 0.6246 (t0) REVERT: B 398 VAL cc_start: 0.8523 (t) cc_final: 0.8259 (p) REVERT: B 404 ARG cc_start: 0.7379 (mtm180) cc_final: 0.7133 (mtm180) REVERT: B 421 VAL cc_start: 0.7829 (t) cc_final: 0.7579 (t) REVERT: B 491 TYR cc_start: 0.7591 (t80) cc_final: 0.7370 (t80) REVERT: B 520 TRP cc_start: 0.7896 (m100) cc_final: 0.7479 (m100) REVERT: C 51 THR cc_start: 0.8641 (t) cc_final: 0.8374 (p) REVERT: C 56 THR cc_start: 0.8262 (p) cc_final: 0.7967 (p) REVERT: C 101 THR cc_start: 0.8143 (t) cc_final: 0.7938 (m) REVERT: D 35 THR cc_start: 0.7562 (m) cc_final: 0.7117 (p) REVERT: D 61 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7360 (mtpt) REVERT: D 169 MET cc_start: 0.8449 (ttp) cc_final: 0.8192 (tmm) REVERT: D 231 ILE cc_start: 0.8541 (mm) cc_final: 0.8245 (tt) REVERT: D 259 LEU cc_start: 0.8517 (mt) cc_final: 0.8269 (mp) REVERT: D 263 VAL cc_start: 0.8592 (t) cc_final: 0.8331 (p) REVERT: D 311 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8120 (ttmm) REVERT: D 318 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7917 (tttp) REVERT: D 324 ASP cc_start: 0.7595 (m-30) cc_final: 0.6698 (m-30) REVERT: D 326 PHE cc_start: 0.8255 (m-80) cc_final: 0.7967 (m-10) REVERT: D 395 ASN cc_start: 0.7450 (p0) cc_final: 0.6986 (p0) REVERT: D 423 LYS cc_start: 0.8402 (mttm) cc_final: 0.8142 (mtmm) REVERT: D 444 PHE cc_start: 0.7928 (t80) cc_final: 0.7678 (t80) REVERT: D 491 TYR cc_start: 0.7950 (t80) cc_final: 0.7642 (t80) REVERT: D 501 MET cc_start: 0.7609 (ttp) cc_final: 0.7279 (ttt) REVERT: D 511 TYR cc_start: 0.8065 (p90) cc_final: 0.7353 (p90) REVERT: D 515 ASP cc_start: 0.6683 (t0) cc_final: 0.6391 (t0) outliers start: 12 outliers final: 12 residues processed: 234 average time/residue: 0.1156 time to fit residues: 37.1803 Evaluate side-chains 236 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 0.0030 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 98 GLN D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102373 restraints weight = 24824.577| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.43 r_work: 0.3126 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11358 Z= 0.139 Angle : 0.499 9.452 15606 Z= 0.255 Chirality : 0.041 0.144 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.606 73.991 2013 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.45 % Allowed : 14.39 % 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: 0.22 (0.24), residues: 1275 helix: 1.19 (0.31), residues: 294 sheet: -1.04 (0.34), residues: 195 loop : 0.17 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 205 TYR 0.020 0.001 TYR D 447 PHE 0.020 0.001 PHE B 444 TRP 0.009 0.001 TRP B 385 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00331 (11317) covalent geometry : angle 0.49336 (15573) hydrogen bonds : bond 0.03494 ( 362) hydrogen bonds : angle 3.90577 ( 962) metal coordination : bond 0.00682 ( 40) metal coordination : angle 1.74923 ( 33) Misc. bond : bond 0.00024 ( 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 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.371 Fit side-chains REVERT: A 5 THR cc_start: 0.8046 (m) cc_final: 0.7562 (m) REVERT: A 6 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7708 (tp30) REVERT: B 65 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7524 (tm-30) REVERT: B 77 GLU cc_start: 0.7374 (mp0) cc_final: 0.7128 (mp0) REVERT: B 122 THR cc_start: 0.8250 (m) cc_final: 0.8008 (p) REVERT: B 139 LYS cc_start: 0.8143 (tttt) cc_final: 0.7862 (ptmm) REVERT: B 153 MET cc_start: 0.8426 (mmm) cc_final: 0.8026 (mmm) REVERT: B 154 TYR cc_start: 0.8137 (m-80) cc_final: 0.7824 (m-80) REVERT: B 212 ARG cc_start: 0.8278 (mtt90) cc_final: 0.8047 (mtt-85) REVERT: B 295 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8272 (mt-10) REVERT: B 310 ARG cc_start: 0.8374 (mtp180) cc_final: 0.8105 (mtp180) REVERT: B 315 MET cc_start: 0.8411 (tpp) cc_final: 0.8157 (tpp) REVERT: B 324 ASP cc_start: 0.7331 (m-30) cc_final: 0.6735 (m-30) REVERT: B 325 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7466 (mmmm) REVERT: B 347 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 349 LYS cc_start: 0.8365 (mttt) cc_final: 0.7936 (mttt) REVERT: B 351 TYR cc_start: 0.8550 (m-80) cc_final: 0.7908 (m-80) REVERT: B 352 ASP cc_start: 0.6874 (t0) cc_final: 0.6251 (t0) REVERT: B 398 VAL cc_start: 0.8576 (t) cc_final: 0.8310 (p) REVERT: B 404 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7085 (mtm180) REVERT: B 421 VAL cc_start: 0.7819 (t) cc_final: 0.7561 (t) REVERT: B 491 TYR cc_start: 0.7631 (t80) cc_final: 0.7401 (t80) REVERT: B 520 TRP cc_start: 0.7923 (m100) cc_final: 0.7525 (m100) REVERT: C 51 THR cc_start: 0.8661 (t) cc_final: 0.8381 (p) REVERT: C 56 THR cc_start: 0.8274 (p) cc_final: 0.7977 (p) REVERT: C 101 THR cc_start: 0.8166 (t) cc_final: 0.7955 (m) REVERT: D 61 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7383 (mtpt) REVERT: D 147 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8000 (mtpp) REVERT: D 169 MET cc_start: 0.8464 (ttp) cc_final: 0.8213 (tmm) REVERT: D 211 ASP cc_start: 0.7822 (t0) cc_final: 0.7411 (t0) REVERT: D 231 ILE cc_start: 0.8537 (mm) cc_final: 0.8245 (tt) REVERT: D 259 LEU cc_start: 0.8503 (mt) cc_final: 0.8271 (mp) REVERT: D 263 VAL cc_start: 0.8580 (t) cc_final: 0.8320 (p) REVERT: D 311 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8151 (ttmm) REVERT: D 318 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7929 (tttp) REVERT: D 324 ASP cc_start: 0.7645 (m-30) cc_final: 0.6755 (m-30) REVERT: D 326 PHE cc_start: 0.8291 (m-80) cc_final: 0.7980 (m-10) REVERT: D 392 TYR cc_start: 0.8713 (m-80) cc_final: 0.8073 (m-80) REVERT: D 395 ASN cc_start: 0.7450 (p0) cc_final: 0.6995 (p0) REVERT: D 423 LYS cc_start: 0.8392 (mttm) cc_final: 0.8105 (mtmm) REVERT: D 444 PHE cc_start: 0.7927 (t80) cc_final: 0.7684 (t80) REVERT: D 491 TYR cc_start: 0.7957 (t80) cc_final: 0.7683 (t80) REVERT: D 501 MET cc_start: 0.7642 (ttp) cc_final: 0.7323 (ttm) REVERT: D 511 TYR cc_start: 0.8029 (p90) cc_final: 0.7357 (p90) REVERT: D 515 ASP cc_start: 0.6697 (t0) cc_final: 0.6394 (t0) outliers start: 16 outliers final: 12 residues processed: 236 average time/residue: 0.1201 time to fit residues: 38.6766 Evaluate side-chains 237 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR 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: 0.9990 chunk 95 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103209 restraints weight = 20854.173| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.22 r_work: 0.3145 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11358 Z= 0.134 Angle : 0.491 9.193 15606 Z= 0.251 Chirality : 0.041 0.147 1740 Planarity : 0.004 0.042 1846 Dihedral : 11.595 73.968 2013 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.36 % Allowed : 14.75 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1275 helix: 1.23 (0.31), residues: 294 sheet: -1.02 (0.34), residues: 195 loop : 0.17 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 205 TYR 0.020 0.001 TYR D 447 PHE 0.020 0.001 PHE B 444 TRP 0.009 0.001 TRP B 385 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00321 (11317) covalent geometry : angle 0.48486 (15573) hydrogen bonds : bond 0.03463 ( 362) hydrogen bonds : angle 3.90527 ( 962) metal coordination : bond 0.00640 ( 40) metal coordination : angle 1.72929 ( 33) Misc. bond : bond 0.00021 ( 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 243 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.385 Fit side-chains REVERT: A 5 THR cc_start: 0.8050 (m) cc_final: 0.7570 (m) REVERT: A 6 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7690 (tp30) REVERT: B 77 GLU cc_start: 0.7331 (mp0) cc_final: 0.7094 (mp0) REVERT: B 122 THR cc_start: 0.8261 (m) cc_final: 0.8010 (p) REVERT: B 139 LYS cc_start: 0.8126 (tttt) cc_final: 0.7879 (ptmm) REVERT: B 153 MET cc_start: 0.8403 (mmm) cc_final: 0.7994 (mmm) REVERT: B 154 TYR cc_start: 0.8137 (m-80) cc_final: 0.7825 (m-80) REVERT: B 212 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8030 (mtt-85) REVERT: B 295 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 310 ARG cc_start: 0.8310 (mtp180) cc_final: 0.8056 (mtp180) REVERT: B 315 MET cc_start: 0.8371 (tpp) cc_final: 0.8116 (tpp) REVERT: B 324 ASP cc_start: 0.7250 (m-30) cc_final: 0.6655 (m-30) REVERT: B 325 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7388 (mmmm) REVERT: B 347 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7103 (mm-30) REVERT: B 349 LYS cc_start: 0.8344 (mttt) cc_final: 0.7939 (mttt) REVERT: B 351 TYR cc_start: 0.8552 (m-80) cc_final: 0.7995 (m-80) REVERT: B 352 ASP cc_start: 0.6854 (t0) cc_final: 0.6224 (t0) REVERT: B 398 VAL cc_start: 0.8521 (t) cc_final: 0.8260 (p) REVERT: B 404 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7133 (mtm180) REVERT: B 421 VAL cc_start: 0.7779 (t) cc_final: 0.7524 (t) REVERT: B 491 TYR cc_start: 0.7611 (t80) cc_final: 0.7376 (t80) REVERT: B 520 TRP cc_start: 0.7915 (m100) cc_final: 0.7525 (m100) REVERT: C 51 THR cc_start: 0.8654 (t) cc_final: 0.8375 (p) REVERT: C 56 THR cc_start: 0.8270 (p) cc_final: 0.7981 (p) REVERT: C 101 THR cc_start: 0.8162 (t) cc_final: 0.7948 (m) REVERT: D 35 THR cc_start: 0.7819 (t) cc_final: 0.7353 (p) REVERT: D 61 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7425 (mtpt) REVERT: D 169 MET cc_start: 0.8456 (ttp) cc_final: 0.8198 (tmm) REVERT: D 211 ASP cc_start: 0.7804 (t0) cc_final: 0.7389 (t0) REVERT: D 231 ILE cc_start: 0.8538 (mm) cc_final: 0.8254 (tt) REVERT: D 259 LEU cc_start: 0.8511 (mt) cc_final: 0.8279 (mp) REVERT: D 263 VAL cc_start: 0.8597 (t) cc_final: 0.8338 (p) REVERT: D 311 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8116 (ttmm) REVERT: D 318 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7931 (tttp) REVERT: D 324 ASP cc_start: 0.7618 (m-30) cc_final: 0.6667 (m-30) REVERT: D 326 PHE cc_start: 0.8276 (m-80) cc_final: 0.7966 (m-10) REVERT: D 395 ASN cc_start: 0.7465 (p0) cc_final: 0.6994 (p0) REVERT: D 423 LYS cc_start: 0.8360 (mttm) cc_final: 0.8085 (mtmm) REVERT: D 444 PHE cc_start: 0.7871 (t80) cc_final: 0.7629 (t80) REVERT: D 491 TYR cc_start: 0.7952 (t80) cc_final: 0.7676 (t80) REVERT: D 501 MET cc_start: 0.7632 (ttp) cc_final: 0.7310 (ttm) REVERT: D 511 TYR cc_start: 0.7961 (p90) cc_final: 0.7265 (p90) REVERT: D 515 ASP cc_start: 0.6761 (t0) cc_final: 0.6458 (t0) outliers start: 15 outliers final: 13 residues processed: 237 average time/residue: 0.1188 time to fit residues: 38.3756 Evaluate side-chains 239 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 341 VAL 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: 0.0870 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.0070 chunk 104 optimal weight: 0.1980 chunk 101 optimal weight: 0.6980 chunk 94 optimal weight: 0.0870 chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104655 restraints weight = 26697.761| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.57 r_work: 0.3155 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- 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 = 0.43 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 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11358 Z= 0.084 Angle : 0.462 8.502 15606 Z= 0.236 Chirality : 0.040 0.145 1740 Planarity : 0.004 0.040 1846 Dihedral : 11.515 73.839 2013 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.63 % Allowed : 15.38 % Favored : 83.98 % 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: 0.33 (0.24), residues: 1275 helix: 1.39 (0.31), residues: 294 sheet: -0.97 (0.36), residues: 173 loop : 0.15 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 205 TYR 0.020 0.001 TYR D 447 PHE 0.022 0.001 PHE B 444 TRP 0.009 0.001 TRP B 385 HIS 0.002 0.000 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00189 (11317) covalent geometry : angle 0.45757 (15573) hydrogen bonds : bond 0.02876 ( 362) hydrogen bonds : angle 3.67611 ( 962) metal coordination : bond 0.00342 ( 40) metal coordination : angle 1.46417 ( 33) Misc. bond : bond 0.00068 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.92 seconds wall clock time: 67 minutes 53.70 seconds (4073.70 seconds total)