Starting phenix.real_space_refine on Thu Sep 18 00:34:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eri_19915/09_2025/9eri_19915.map" } resolution = 3.3 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= 0.006 sd= 0.204 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 42 7.16 5 P 5 5.49 5 S 158 5.16 5 C 8095 2.51 5 N 2070 2.21 5 O 2334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12704 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1433 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2394 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3287 Classifications: {'peptide': 443} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 413} Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2374 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 302} Chain: "E" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1439 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "G" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1531 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 201} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {'FMN': 1, 'NAD': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 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 199 SG CYS A 25 38.766 88.923 48.270 1.00 20.75 S ATOM 10283 SG CYS E 108 40.921 87.923 45.540 1.00 35.69 S ATOM 857 SG CYS A 113 40.166 93.282 43.175 1.00 36.08 S ATOM 9687 SG CYS E 25 38.404 93.580 46.318 1.00 28.53 S ATOM 2824 SG CYS B 200 34.689 55.626 95.402 1.00 19.73 S ATOM 2373 SG CYS B 138 35.115 61.700 97.448 1.00 14.43 S ATOM 2927 SG CYS B 213 29.589 58.719 97.238 1.00 31.13 S ATOM 2142 SG CYS B 106 32.701 60.655 91.664 1.00 17.49 S ATOM 2406 SG CYS B 142 32.490 65.400 88.130 1.00 12.07 S ATOM 2288 SG CYS B 125 35.134 70.857 86.679 1.00 18.05 S ATOM 2447 SG CYS B 148 34.322 66.963 82.047 1.00 17.90 S ATOM 2688 SG CYS B 182 38.892 65.528 86.117 1.00 14.93 S ATOM 1945 SG CYS B 75 45.404 61.486 64.393 1.00 77.94 S ATOM 1811 SG CYS B 53 48.360 65.121 67.922 1.00 84.68 S ATOM 1797 SG CYS B 50 42.232 66.627 67.202 1.00 68.02 S ATOM 1840 SG CYS B 58 45.724 66.530 61.686 1.00 80.60 S ATOM 2642 SG CYS B 175 40.389 64.737 72.397 1.00 23.00 S ATOM 2661 SG CYS B 178 38.172 63.500 78.193 1.00 16.28 S ATOM 2623 SG CYS B 172 35.883 59.855 73.552 1.00 26.61 S ATOM 2474 SG CYS B 152 34.911 66.462 73.480 1.00 16.91 S ATOM 3219 SG CYS B 252 34.759 42.591 89.294 1.00 42.93 S ATOM 3192 SG CYS B 249 35.275 36.938 86.930 1.00 50.79 S ATOM 3013 SG CYS B 227 40.083 38.953 89.210 1.00 46.03 S ATOM 3166 SG CYS B 246 37.933 42.487 83.878 1.00 44.96 S ATOM 2952 SG CYS B 217 37.452 50.568 97.016 1.00 30.73 S ATOM 2971 SG CYS B 220 35.355 45.286 100.515 1.00 35.20 S ATOM 2986 SG CYS B 223 37.959 44.534 95.067 1.00 41.15 S ATOM 3249 SG CYS B 256 32.021 46.873 95.659 1.00 41.00 S ATOM 3278 SG CYS B 260 32.587 48.500 95.335 1.00 35.65 S ATOM 3488 SG CYS B 289 34.213 22.900 83.450 1.00 96.73 S ATOM 3668 SG CYS B 313 35.481 29.772 83.575 1.00 86.37 S ATOM 3720 SG CYS B 320 37.253 23.097 72.780 1.00 95.77 S ATOM 3442 SG CYS B 282 37.438 16.342 72.210 1.00108.27 S ATOM 3423 SG CYS B 279 34.864 17.784 70.534 1.00 99.22 S ATOM 3442 SG CYS B 282 37.438 16.342 72.210 1.00108.27 S ATOM 6541 SG CYS C 369 37.494 94.382 82.139 1.00 22.39 S ATOM 6565 SG CYS C 372 38.129 99.653 86.084 1.00 21.92 S ATOM 6584 SG CYS C 375 42.750 95.661 85.756 1.00 25.13 S ATOM 6915 SG CYS C 418 36.971 94.126 88.545 1.00 11.76 S ATOM 6608 SG CYS C 379 48.905 94.320 88.927 1.00 22.69 S ATOM 6844 SG CYS C 408 49.733 87.754 90.930 1.00 19.88 S ATOM 6883 SG CYS C 414 44.481 91.291 90.712 1.00 18.46 S ATOM 6867 SG CYS C 411 48.908 92.452 95.104 1.00 15.14 S Time building chain proxies: 3.23, per 1000 atoms: 0.25 Number of scatterers: 12704 At special positions: 0 Unit cell: (89.38, 148.24, 143.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 42 26.01 S 158 16.00 P 5 15.00 O 2334 8.00 N 2070 7.00 C 8095 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 621.1 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 108 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 201 " - pdb=" SG CYS E 25 " pdb=" SF4 B 401 " pdb="FE4 SF4 B 401 " - pdb=" SG CYS B 106 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 138 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 213 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 200 " pdb=" SF4 B 402 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 125 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 142 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 148 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 182 " pdb=" SF4 B 403 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 58 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 75 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 53 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 50 " pdb=" SF4 B 404 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 178 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 175 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 172 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 152 " pdb=" SF4 B 405 " pdb="FE2 SF4 B 405 " - pdb=" SG CYS B 249 " pdb="FE1 SF4 B 405 " - pdb=" SG CYS B 252 " pdb="FE4 SF4 B 405 " - pdb=" SG CYS B 246 " pdb="FE3 SF4 B 405 " - pdb=" SG CYS B 227 " pdb=" SF4 B 406 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 260 " pdb="FE2 SF4 B 406 " - pdb=" SG CYS B 220 " pdb="FE1 SF4 B 406 " - pdb=" SG CYS B 217 " pdb="FE3 SF4 B 406 " - pdb=" SG CYS B 223 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 256 " pdb=" SF4 B 407 " pdb="FE4 SF4 B 407 " - pdb=" SG CYS B 313 " pdb="FE3 SF4 B 407 " - pdb=" SG CYS B 289 " pdb="FE2 SF4 B 407 " - pdb=" SG CYS B 316 " pdb=" SF4 B 408 " pdb="FE1 SF4 B 408 " - pdb=" SG CYS B 320 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 282 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 279 " pdb=" SF4 C 503 " pdb="FE4 SF4 C 503 " - pdb=" SG CYS C 418 " pdb="FE3 SF4 C 503 " - pdb=" SG CYS C 375 " pdb="FE1 SF4 C 503 " - pdb=" SG CYS C 369 " pdb="FE2 SF4 C 503 " - pdb=" SG CYS C 372 " pdb=" SF4 C 504 " pdb="FE4 SF4 C 504 " - pdb=" SG CYS C 411 " pdb="FE1 SF4 C 504 " - pdb=" SG CYS C 379 " pdb="FE3 SF4 C 504 " - pdb=" SG CYS C 414 " pdb="FE2 SF4 C 504 " - pdb=" SG CYS C 408 " Number of angles added : 123 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 13 sheets defined 50.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 60 removed outlier: 3.533A pdb=" N TYR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.639A pdb=" N LEU A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 removed outlier: 4.435A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.572A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.733A pdb=" N LEU A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 158 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.531A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'B' and resid 2 through 30 Proline residue: B 8 - end of helix removed outlier: 3.921A pdb=" N VAL B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 4.638A pdb=" N CYS B 75 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 4.032A pdb=" N CYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.755A pdb=" N LYS C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.534A pdb=" N HIS C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.519A pdb=" N VAL C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.571A pdb=" N CYS C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.999A pdb=" N GLU C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.762A pdb=" N CYS C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.132A pdb=" N SER C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 42 Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 43 through 68 removed outlier: 4.207A pdb=" N LEU D 47 " --> pdb=" O GLY D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.826A pdb=" N ASP D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 95 through 109 removed outlier: 3.583A pdb=" N GLY D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.527A pdb=" N GLY D 115 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.547A pdb=" N LEU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 removed outlier: 4.254A pdb=" N SER D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 209 through 227 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 256 through 278 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 23 through 30 removed outlier: 3.629A pdb=" N THR E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 58 Processing helix chain 'E' and resid 66 through 90 Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.567A pdb=" N ASP E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 Proline residue: E 102 - end of helix removed outlier: 3.732A pdb=" N VAL E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 105' Processing helix chain 'E' and resid 107 through 117 removed outlier: 3.758A pdb=" N LEU E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 154 Processing helix chain 'E' and resid 174 through 196 Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 11 through 59 removed outlier: 3.730A pdb=" N GLY G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLY G 41 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 80 removed outlier: 3.579A pdb=" N ALA G 77 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.693A pdb=" N ALA G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 148' Processing helix chain 'G' and resid 150 through 156 Processing helix chain 'G' and resid 187 through 207 removed outlier: 3.892A pdb=" N THR G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 207 " --> pdb=" O GLN G 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 103 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 7.196A pdb=" N GLU B 118 " --> pdb=" O VAL D 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 3.554A pdb=" N ILE B 197 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274 removed outlier: 4.209A pdb=" N TYR B 273 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 5.805A pdb=" N LYS C 4 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY C 202 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR C 230 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE C 204 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU C 232 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C 206 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS C 160 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N MET C 267 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 162 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.531A pdb=" N ALA C 84 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU C 102 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL C 82 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.703A pdb=" N THR C 48 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 65 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 74 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 301 through 306 removed outlier: 8.372A pdb=" N ILE C 353 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR C 291 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS C 355 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 293 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR C 357 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY C 352 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 330 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 354 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 328 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 356 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 337 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 64 through 67 removed outlier: 3.836A pdb=" N GLU G 90 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY G 102 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER G 96 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR G 107 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 119 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY G 131 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER G 124 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 129 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 165 through 167 606 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.34: 3876 1.34 - 1.57: 8793 1.57 - 1.81: 171 1.81 - 2.05: 6 2.05 - 2.28: 124 Bond restraints: 12970 Sorted by residual: bond pdb=" C4 RBF D 401 " pdb=" N3 RBF D 401 " ideal model delta sigma weight residual 1.362 1.150 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C2 RBF D 401 " pdb=" N3 RBF D 401 " ideal model delta sigma weight residual 1.397 1.219 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C3D NAD C 502 " pdb=" C4D NAD C 502 " ideal model delta sigma weight residual 1.531 1.404 0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C8 RBF D 401 " pdb=" C8M RBF D 401 " ideal model delta sigma weight residual 1.496 1.371 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O3 NAD C 502 " pdb=" PA NAD C 502 " ideal model delta sigma weight residual 1.653 1.533 0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 12965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 17648 7.09 - 14.19: 42 14.19 - 21.28: 5 21.28 - 28.37: 4 28.37 - 35.47: 2 Bond angle restraints: 17701 Sorted by residual: angle pdb=" N3 RBF D 401 " pdb=" C4 RBF D 401 " pdb=" O4 RBF D 401 " ideal model delta sigma weight residual 123.36 87.89 35.47 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C1' RBF D 401 " pdb=" C2' RBF D 401 " pdb=" C3' RBF D 401 " ideal model delta sigma weight residual 110.21 140.71 -30.50 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C3' RBF D 401 " pdb=" C2' RBF D 401 " pdb=" O2' RBF D 401 " ideal model delta sigma weight residual 111.96 84.09 27.87 3.00e+00 1.11e-01 8.63e+01 angle pdb=" C2B NAD C 502 " pdb=" C1B NAD C 502 " pdb=" N9A NAD C 502 " ideal model delta sigma weight residual 114.24 140.34 -26.10 3.00e+00 1.11e-01 7.57e+01 angle pdb=" O1P FMN D 402 " pdb=" P FMN D 402 " pdb=" O2P FMN D 402 " ideal model delta sigma weight residual 112.53 89.37 23.16 3.00e+00 1.11e-01 5.96e+01 ... (remaining 17696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6845 17.93 - 35.85: 657 35.85 - 53.78: 193 53.78 - 71.71: 27 71.71 - 89.63: 13 Dihedral angle restraints: 7735 sinusoidal: 2959 harmonic: 4776 Sorted by residual: dihedral pdb=" CA CYS B 289 " pdb=" C CYS B 289 " pdb=" N PRO B 290 " pdb=" CA PRO B 290 " ideal model delta harmonic sigma weight residual 180.00 -146.87 -33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA LEU A 98 " pdb=" C LEU A 98 " pdb=" N TYR A 99 " pdb=" CA TYR A 99 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ILE D 146 " pdb=" C ILE D 146 " pdb=" N PRO D 147 " pdb=" CA PRO D 147 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2124 0.128 - 0.256: 16 0.256 - 0.385: 2 0.385 - 0.513: 2 0.513 - 0.641: 1 Chirality restraints: 2145 Sorted by residual: chirality pdb=" C2D NAD C 502 " pdb=" C1D NAD C 502 " pdb=" C3D NAD C 502 " pdb=" O2D NAD C 502 " both_signs ideal model delta sigma weight residual False -2.56 -1.92 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1B NAD C 502 " pdb=" C2B NAD C 502 " pdb=" N9A NAD C 502 " pdb=" O4B NAD C 502 " both_signs ideal model delta sigma weight residual False 2.35 1.88 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C3D NAD C 502 " pdb=" C2D NAD C 502 " pdb=" C4D NAD C 502 " pdb=" O3D NAD C 502 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 2142 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' RBF D 401 " 0.046 2.00e-02 2.50e+03 6.41e-02 1.95e+02 pdb=" C10 RBF D 401 " 0.053 2.00e-02 2.50e+03 pdb=" C2 RBF D 401 " 0.037 2.00e-02 2.50e+03 pdb=" C4 RBF D 401 " 0.068 2.00e-02 2.50e+03 pdb=" C4A RBF D 401 " 0.048 2.00e-02 2.50e+03 pdb=" C5A RBF D 401 " 0.011 2.00e-02 2.50e+03 pdb=" C6 RBF D 401 " -0.009 2.00e-02 2.50e+03 pdb=" C7 RBF D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C7M RBF D 401 " -0.048 2.00e-02 2.50e+03 pdb=" C8 RBF D 401 " -0.021 2.00e-02 2.50e+03 pdb=" C8M RBF D 401 " -0.039 2.00e-02 2.50e+03 pdb=" C9 RBF D 401 " -0.001 2.00e-02 2.50e+03 pdb=" C9A RBF D 401 " 0.016 2.00e-02 2.50e+03 pdb=" N1 RBF D 401 " 0.070 2.00e-02 2.50e+03 pdb=" N10 RBF D 401 " 0.041 2.00e-02 2.50e+03 pdb=" N3 RBF D 401 " -0.040 2.00e-02 2.50e+03 pdb=" N5 RBF D 401 " 0.026 2.00e-02 2.50e+03 pdb=" O2 RBF D 401 " -0.225 2.00e-02 2.50e+03 pdb=" O4 RBF D 401 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 84 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C LYS G 84 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS G 84 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 85 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 68 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO G 69 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 69 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 69 " -0.030 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1536 2.75 - 3.29: 11959 3.29 - 3.83: 20296 3.83 - 4.36: 22704 4.36 - 4.90: 40979 Nonbonded interactions: 97474 Sorted by model distance: nonbonded pdb=" O4' RBF D 401 " pdb=" O5' RBF D 401 " model vdw 2.216 2.432 nonbonded pdb=" O SER B 185 " pdb=" OG SER B 185 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP B 124 " pdb=" OG1 THR B 147 " model vdw 2.254 3.040 nonbonded pdb=" ND2 ASN C 268 " pdb=" O2 FMN C 501 " model vdw 2.298 3.120 nonbonded pdb=" OD1 ASN A 122 " pdb=" ND2 ASN A 135 " model vdw 2.314 3.120 ... (remaining 97469 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.011 1.061 13018 Z= 0.401 Angle : 1.519 68.604 17824 Z= 0.459 Chirality : 0.050 0.641 2145 Planarity : 0.005 0.064 2172 Dihedral : 15.826 89.633 4685 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.43 % Favored : 94.03 % Rotamer: Outliers : 1.86 % Allowed : 17.30 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.60 (0.20), residues: 1676 helix: 0.54 (0.19), residues: 790 sheet: -0.29 (0.51), residues: 107 loop : -1.39 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 13 TYR 0.018 0.001 TYR D 40 PHE 0.010 0.001 PHE B 30 TRP 0.007 0.001 TRP D 97 HIS 0.003 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00584 (12970) covalent geometry : angle 1.03787 (17701) hydrogen bonds : bond 0.14901 ( 606) hydrogen bonds : angle 6.04391 ( 1773) metal coordination : bond 0.16197 ( 43) metal coordination : angle 13.39230 ( 123) Misc. bond : bond 0.02917 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6646 (m-80) cc_final: 0.6080 (m-80) REVERT: B 92 MET cc_start: 0.0785 (pmm) cc_final: -0.1216 (ptp) REVERT: B 309 MET cc_start: 0.0329 (ppp) cc_final: 0.0029 (pmm) REVERT: C 116 TYR cc_start: 0.8172 (m-80) cc_final: 0.7956 (m-80) REVERT: C 343 ASP cc_start: 0.7143 (t0) cc_final: 0.6747 (t0) REVERT: D 66 LYS cc_start: 0.7723 (tppt) cc_final: 0.7225 (ttmt) REVERT: D 174 ASP cc_start: 0.7804 (t0) cc_final: 0.7435 (t0) REVERT: E 4 MET cc_start: 0.5110 (mmt) cc_final: 0.4864 (mmt) outliers start: 25 outliers final: 21 residues processed: 165 average time/residue: 0.1178 time to fit residues: 27.7231 Evaluate side-chains 163 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 192 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.199128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143903 restraints weight = 13743.139| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.82 r_work: 0.3394 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13018 Z= 0.106 Angle : 1.069 65.713 17824 Z= 0.292 Chirality : 0.042 0.218 2145 Planarity : 0.004 0.045 2172 Dihedral : 7.861 85.755 1898 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.13 % Favored : 94.33 % Rotamer: Outliers : 3.12 % Allowed : 16.11 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.07 (0.21), residues: 1676 helix: 1.35 (0.19), residues: 790 sheet: -0.15 (0.53), residues: 107 loop : -1.33 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.016 0.001 TYR D 40 PHE 0.008 0.001 PHE B 30 TRP 0.007 0.001 TRP D 97 HIS 0.002 0.000 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00214 (12970) covalent geometry : angle 0.53743 (17701) hydrogen bonds : bond 0.03754 ( 606) hydrogen bonds : angle 4.45171 ( 1773) metal coordination : bond 0.00600 ( 43) metal coordination : angle 11.13502 ( 123) Misc. bond : bond 0.00107 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7011 (m-80) cc_final: 0.6369 (m-80) REVERT: B 155 ASP cc_start: 0.8328 (t70) cc_final: 0.7795 (t70) REVERT: B 245 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8032 (mtmm) REVERT: C 116 TYR cc_start: 0.7918 (m-80) cc_final: 0.7326 (m-80) REVERT: C 122 MET cc_start: 0.7870 (mmm) cc_final: 0.7069 (tmm) REVERT: C 201 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7323 (mmmt) REVERT: C 343 ASP cc_start: 0.7924 (t0) cc_final: 0.7456 (t0) REVERT: C 347 MET cc_start: 0.8308 (mmt) cc_final: 0.8035 (mmm) REVERT: D 66 LYS cc_start: 0.7553 (tppt) cc_final: 0.6676 (ttmt) REVERT: D 129 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.5224 (tpp-160) REVERT: D 174 ASP cc_start: 0.7597 (t0) cc_final: 0.7095 (t0) REVERT: E 4 MET cc_start: 0.4825 (mmt) cc_final: 0.4551 (mmt) outliers start: 42 outliers final: 15 residues processed: 193 average time/residue: 0.1216 time to fit residues: 33.7134 Evaluate side-chains 159 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 48 optimal weight: 0.0040 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.195602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140542 restraints weight = 13830.733| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.10 r_work: 0.3317 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13018 Z= 0.136 Angle : 1.046 63.870 17824 Z= 0.300 Chirality : 0.043 0.201 2145 Planarity : 0.004 0.043 2172 Dihedral : 7.462 88.601 1878 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.49 % Favored : 94.03 % Rotamer: Outliers : 2.60 % Allowed : 17.15 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1676 helix: 1.41 (0.19), residues: 805 sheet: -0.14 (0.53), residues: 107 loop : -1.32 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 13 TYR 0.016 0.001 TYR D 263 PHE 0.008 0.001 PHE D 131 TRP 0.007 0.001 TRP D 45 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00324 (12970) covalent geometry : angle 0.56304 (17701) hydrogen bonds : bond 0.04089 ( 606) hydrogen bonds : angle 4.30697 ( 1773) metal coordination : bond 0.00719 ( 43) metal coordination : angle 10.62554 ( 123) Misc. bond : bond 0.00097 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7540 (m-80) cc_final: 0.6931 (m-80) REVERT: B 245 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: B 309 MET cc_start: 0.1611 (ppp) cc_final: 0.1402 (pmm) REVERT: C 116 TYR cc_start: 0.8001 (m-80) cc_final: 0.7452 (m-80) REVERT: C 122 MET cc_start: 0.8005 (mmm) cc_final: 0.7283 (mmm) REVERT: C 201 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7348 (mmmt) REVERT: C 343 ASP cc_start: 0.8049 (t0) cc_final: 0.7622 (t0) REVERT: D 66 LYS cc_start: 0.7714 (tppt) cc_final: 0.6837 (ttpt) REVERT: D 129 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.5529 (tpp-160) REVERT: D 174 ASP cc_start: 0.7649 (t0) cc_final: 0.6985 (t0) REVERT: E 1 MET cc_start: 0.4852 (pmm) cc_final: 0.4457 (tmm) REVERT: E 4 MET cc_start: 0.4828 (mmt) cc_final: 0.4568 (mmt) REVERT: E 90 VAL cc_start: 0.7009 (t) cc_final: 0.6570 (m) outliers start: 35 outliers final: 23 residues processed: 191 average time/residue: 0.1169 time to fit residues: 32.1829 Evaluate side-chains 171 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 185 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 80 optimal weight: 0.2980 chunk 154 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.196975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141482 restraints weight = 13778.852| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.03 r_work: 0.3341 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13018 Z= 0.108 Angle : 0.991 60.954 17824 Z= 0.284 Chirality : 0.043 0.282 2145 Planarity : 0.004 0.043 2172 Dihedral : 7.242 87.270 1878 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.25 % Favored : 94.27 % Rotamer: Outliers : 3.27 % Allowed : 16.93 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1676 helix: 1.56 (0.19), residues: 805 sheet: -0.12 (0.53), residues: 108 loop : -1.27 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.013 0.001 TYR D 215 PHE 0.007 0.001 PHE D 131 TRP 0.008 0.001 TRP D 97 HIS 0.002 0.000 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00237 (12970) covalent geometry : angle 0.52841 (17701) hydrogen bonds : bond 0.03584 ( 606) hydrogen bonds : angle 4.14966 ( 1773) metal coordination : bond 0.00539 ( 43) metal coordination : angle 10.11216 ( 123) Misc. bond : bond 0.00085 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5610 (m-80) REVERT: A 127 TYR cc_start: 0.7617 (m-80) cc_final: 0.7058 (m-80) REVERT: B 92 MET cc_start: 0.0096 (pmm) cc_final: -0.1101 (ppp) REVERT: B 245 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8170 (mttp) REVERT: C 116 TYR cc_start: 0.8027 (m-80) cc_final: 0.7425 (m-80) REVERT: C 122 MET cc_start: 0.7891 (mmm) cc_final: 0.7079 (mmm) REVERT: C 201 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7341 (mmmt) REVERT: C 343 ASP cc_start: 0.8067 (t0) cc_final: 0.7658 (t0) REVERT: D 66 LYS cc_start: 0.7655 (tppt) cc_final: 0.6757 (ttmt) REVERT: D 129 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6099 (tpp-160) REVERT: D 174 ASP cc_start: 0.7653 (t0) cc_final: 0.7128 (t0) REVERT: E 1 MET cc_start: 0.5197 (pmm) cc_final: 0.4761 (tmm) REVERT: E 4 MET cc_start: 0.4908 (mmt) cc_final: 0.4585 (tpp) REVERT: E 90 VAL cc_start: 0.6984 (t) cc_final: 0.6598 (m) outliers start: 44 outliers final: 27 residues processed: 186 average time/residue: 0.1247 time to fit residues: 33.2310 Evaluate side-chains 177 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 316 CYS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 185 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.194167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138306 restraints weight = 13626.407| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.02 r_work: 0.3340 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13018 Z= 0.109 Angle : 1.171 66.526 17824 Z= 0.286 Chirality : 0.042 0.215 2145 Planarity : 0.004 0.044 2172 Dihedral : 7.063 87.396 1875 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.37 % Favored : 94.15 % Rotamer: Outliers : 3.12 % Allowed : 17.07 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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 aren not related in a simple way. whole: 0.37 (0.21), residues: 1676 helix: 1.65 (0.19), residues: 805 sheet: -0.07 (0.54), residues: 107 loop : -1.29 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.013 0.001 TYR D 263 PHE 0.007 0.001 PHE D 131 TRP 0.005 0.001 TRP D 45 HIS 0.002 0.000 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00242 (12970) covalent geometry : angle 0.52166 (17701) hydrogen bonds : bond 0.03545 ( 606) hydrogen bonds : angle 4.05206 ( 1773) metal coordination : bond 0.00930 ( 43) metal coordination : angle 12.63669 ( 123) Misc. bond : bond 0.00078 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5570 (m-80) REVERT: A 122 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7468 (t0) REVERT: B 92 MET cc_start: 0.0218 (OUTLIER) cc_final: -0.1243 (ppp) REVERT: B 245 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: C 116 TYR cc_start: 0.8048 (m-80) cc_final: 0.7446 (m-80) REVERT: C 122 MET cc_start: 0.8032 (mmm) cc_final: 0.7153 (mmm) REVERT: C 201 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7349 (mmmt) REVERT: C 343 ASP cc_start: 0.8086 (t0) cc_final: 0.7663 (t0) REVERT: C 347 MET cc_start: 0.8314 (mmm) cc_final: 0.7894 (mmm) REVERT: D 66 LYS cc_start: 0.7888 (tppt) cc_final: 0.6976 (ttmt) REVERT: D 129 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6203 (tpp-160) REVERT: D 174 ASP cc_start: 0.7888 (t0) cc_final: 0.7187 (t0) REVERT: E 1 MET cc_start: 0.5112 (pmm) cc_final: 0.4832 (tmm) REVERT: E 4 MET cc_start: 0.4907 (mmt) cc_final: 0.4581 (tpp) REVERT: E 90 VAL cc_start: 0.6993 (t) cc_final: 0.6639 (m) outliers start: 42 outliers final: 28 residues processed: 189 average time/residue: 0.1236 time to fit residues: 33.5077 Evaluate side-chains 184 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 316 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.191353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136313 restraints weight = 13515.259| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.89 r_work: 0.3309 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13018 Z= 0.140 Angle : 1.184 65.111 17824 Z= 0.303 Chirality : 0.044 0.221 2145 Planarity : 0.004 0.044 2172 Dihedral : 7.168 89.484 1874 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.91 % Favored : 93.62 % Rotamer: Outliers : 3.64 % Allowed : 17.30 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1676 helix: 1.66 (0.19), residues: 798 sheet: -0.03 (0.54), residues: 107 loop : -1.26 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.018 0.001 TYR D 215 PHE 0.010 0.001 PHE D 131 TRP 0.006 0.001 TRP D 45 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00339 (12970) covalent geometry : angle 0.55705 (17701) hydrogen bonds : bond 0.04045 ( 606) hydrogen bonds : angle 4.10708 ( 1773) metal coordination : bond 0.01058 ( 43) metal coordination : angle 12.58448 ( 123) Misc. bond : bond 0.00100 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5693 (m-80) REVERT: A 122 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 92 MET cc_start: 0.0338 (OUTLIER) cc_final: -0.1436 (ppp) REVERT: B 230 ASP cc_start: 0.8516 (t0) cc_final: 0.8206 (t0) REVERT: B 245 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: C 107 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: C 116 TYR cc_start: 0.8064 (m-80) cc_final: 0.7495 (m-80) REVERT: C 121 ASP cc_start: 0.8199 (t0) cc_final: 0.7999 (t0) REVERT: C 122 MET cc_start: 0.8122 (mmm) cc_final: 0.7276 (mmm) REVERT: C 201 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7544 (mmmt) REVERT: C 304 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 343 ASP cc_start: 0.8187 (t0) cc_final: 0.7573 (t0) REVERT: D 66 LYS cc_start: 0.7941 (tppt) cc_final: 0.7000 (ttpt) REVERT: D 129 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6241 (tpp-160) REVERT: D 174 ASP cc_start: 0.7958 (t0) cc_final: 0.7161 (t0) REVERT: E 1 MET cc_start: 0.5106 (pmm) cc_final: 0.4904 (tmm) REVERT: E 4 MET cc_start: 0.5032 (mmt) cc_final: 0.4751 (mmt) REVERT: E 90 VAL cc_start: 0.7023 (t) cc_final: 0.6691 (m) outliers start: 49 outliers final: 32 residues processed: 205 average time/residue: 0.1180 time to fit residues: 34.7759 Evaluate side-chains 196 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 316 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 131 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.188783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133661 restraints weight = 13638.844| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.06 r_work: 0.3263 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13018 Z= 0.174 Angle : 1.211 62.584 17824 Z= 0.319 Chirality : 0.045 0.213 2145 Planarity : 0.004 0.044 2172 Dihedral : 7.186 88.078 1873 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.62 % Favored : 92.96 % Rotamer: Outliers : 3.64 % Allowed : 17.45 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1676 helix: 1.55 (0.19), residues: 797 sheet: -0.14 (0.53), residues: 107 loop : -1.29 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 13 TYR 0.020 0.001 TYR D 263 PHE 0.012 0.001 PHE D 131 TRP 0.006 0.001 TRP D 45 HIS 0.003 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00433 (12970) covalent geometry : angle 0.59024 (17701) hydrogen bonds : bond 0.04522 ( 606) hydrogen bonds : angle 4.20849 ( 1773) metal coordination : bond 0.01197 ( 43) metal coordination : angle 12.73922 ( 123) Misc. bond : bond 0.00145 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.0154 (OUTLIER) cc_final: -0.1580 (ppp) REVERT: B 129 MET cc_start: 0.7927 (tpt) cc_final: 0.7090 (tpt) REVERT: B 230 ASP cc_start: 0.8675 (t0) cc_final: 0.8281 (t0) REVERT: B 245 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8131 (mttp) REVERT: C 52 LYS cc_start: 0.8123 (pttt) cc_final: 0.7905 (ptpp) REVERT: C 107 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: C 116 TYR cc_start: 0.8126 (m-80) cc_final: 0.7549 (m-80) REVERT: C 122 MET cc_start: 0.8167 (mmm) cc_final: 0.7176 (mmm) REVERT: C 201 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7574 (mmmt) REVERT: C 304 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 334 MET cc_start: 0.8972 (mmm) cc_final: 0.8689 (mmm) REVERT: C 343 ASP cc_start: 0.8288 (t0) cc_final: 0.7722 (t0) REVERT: C 347 MET cc_start: 0.8479 (mmm) cc_final: 0.8256 (mmm) REVERT: D 66 LYS cc_start: 0.7979 (tppt) cc_final: 0.7040 (ttpt) REVERT: D 129 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6300 (tpp-160) REVERT: D 174 ASP cc_start: 0.7850 (t0) cc_final: 0.7044 (t0) REVERT: E 4 MET cc_start: 0.5078 (mmt) cc_final: 0.4807 (mmt) REVERT: E 90 VAL cc_start: 0.6903 (t) cc_final: 0.6539 (m) outliers start: 49 outliers final: 34 residues processed: 199 average time/residue: 0.1226 time to fit residues: 34.8989 Evaluate side-chains 196 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.193041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137799 restraints weight = 13720.207| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.13 r_work: 0.3282 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13018 Z= 0.132 Angle : 1.174 61.428 17824 Z= 0.302 Chirality : 0.043 0.227 2145 Planarity : 0.004 0.044 2172 Dihedral : 6.973 89.231 1873 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.15 % Favored : 93.50 % Rotamer: Outliers : 3.41 % Allowed : 18.11 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1676 helix: 1.65 (0.19), residues: 794 sheet: -0.07 (0.56), residues: 97 loop : -1.22 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 13 TYR 0.016 0.001 TYR A 56 PHE 0.017 0.001 PHE A 21 TRP 0.006 0.001 TRP D 97 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00312 (12970) covalent geometry : angle 0.55816 (17701) hydrogen bonds : bond 0.03975 ( 606) hydrogen bonds : angle 4.11912 ( 1773) metal coordination : bond 0.00901 ( 43) metal coordination : angle 12.44473 ( 123) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.0150 (OUTLIER) cc_final: -0.1521 (ppp) REVERT: B 129 MET cc_start: 0.7769 (tpt) cc_final: 0.6903 (tpt) REVERT: B 230 ASP cc_start: 0.8810 (t0) cc_final: 0.8505 (t0) REVERT: B 245 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8088 (mttp) REVERT: C 52 LYS cc_start: 0.8068 (pttt) cc_final: 0.7850 (ptpp) REVERT: C 107 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: C 122 MET cc_start: 0.8260 (mmm) cc_final: 0.7298 (mmm) REVERT: C 201 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7576 (mmmt) REVERT: C 304 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 334 MET cc_start: 0.8960 (mmm) cc_final: 0.8652 (mmm) REVERT: C 343 ASP cc_start: 0.8324 (t0) cc_final: 0.7739 (t0) REVERT: C 347 MET cc_start: 0.8404 (mmm) cc_final: 0.8176 (mmm) REVERT: D 66 LYS cc_start: 0.8026 (tppt) cc_final: 0.7096 (ttpt) REVERT: D 129 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6281 (tpp-160) REVERT: D 174 ASP cc_start: 0.7831 (t0) cc_final: 0.7014 (t0) REVERT: E 4 MET cc_start: 0.5121 (mmt) cc_final: 0.4867 (mmt) REVERT: E 90 VAL cc_start: 0.6754 (t) cc_final: 0.6392 (m) outliers start: 46 outliers final: 32 residues processed: 196 average time/residue: 0.1264 time to fit residues: 35.4997 Evaluate side-chains 190 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131306 restraints weight = 13620.958| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.27 r_work: 0.3222 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13018 Z= 0.204 Angle : 1.232 60.293 17824 Z= 0.335 Chirality : 0.047 0.251 2145 Planarity : 0.004 0.044 2172 Dihedral : 7.151 89.101 1873 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.52 % Favored : 92.18 % Rotamer: Outliers : 3.64 % Allowed : 18.19 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 aren not related in a simple way. whole: 0.14 (0.21), residues: 1676 helix: 1.46 (0.19), residues: 789 sheet: -0.24 (0.56), residues: 97 loop : -1.34 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 226 TYR 0.022 0.002 TYR D 215 PHE 0.023 0.001 PHE A 21 TRP 0.005 0.001 TRP D 45 HIS 0.004 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00513 (12970) covalent geometry : angle 0.62806 (17701) hydrogen bonds : bond 0.04894 ( 606) hydrogen bonds : angle 4.28774 ( 1773) metal coordination : bond 0.01363 ( 43) metal coordination : angle 12.77136 ( 123) Misc. bond : bond 0.00128 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.0139 (OUTLIER) cc_final: -0.1481 (ppp) REVERT: B 129 MET cc_start: 0.7944 (tpt) cc_final: 0.7106 (tpt) REVERT: B 230 ASP cc_start: 0.8853 (t0) cc_final: 0.8440 (t0) REVERT: B 245 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: B 309 MET cc_start: 0.1807 (pmm) cc_final: 0.1330 (pmm) REVERT: C 52 LYS cc_start: 0.8022 (pttt) cc_final: 0.7816 (ptpp) REVERT: C 107 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: C 122 MET cc_start: 0.8287 (mmm) cc_final: 0.7383 (mmm) REVERT: C 201 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7607 (mmmt) REVERT: C 226 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7366 (mtm110) REVERT: C 292 CYS cc_start: 0.7345 (t) cc_final: 0.6860 (p) REVERT: C 304 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 334 MET cc_start: 0.8993 (mmm) cc_final: 0.8692 (mmm) REVERT: C 343 ASP cc_start: 0.8340 (t0) cc_final: 0.7896 (t0) REVERT: C 347 MET cc_start: 0.8457 (mmm) cc_final: 0.8231 (mmm) REVERT: D 66 LYS cc_start: 0.8002 (tppt) cc_final: 0.7071 (ttpt) REVERT: D 129 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6283 (tpp-160) REVERT: D 174 ASP cc_start: 0.7810 (t0) cc_final: 0.7337 (t0) REVERT: E 4 MET cc_start: 0.5500 (mmt) cc_final: 0.5207 (mmt) REVERT: E 90 VAL cc_start: 0.6709 (t) cc_final: 0.6301 (m) outliers start: 49 outliers final: 35 residues processed: 198 average time/residue: 0.1273 time to fit residues: 36.1801 Evaluate side-chains 198 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 0.0570 chunk 122 optimal weight: 0.5980 chunk 121 optimal weight: 0.0030 chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN G 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.196783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142345 restraints weight = 13775.875| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.16 r_work: 0.3337 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13018 Z= 0.103 Angle : 1.133 60.778 17824 Z= 0.293 Chirality : 0.043 0.313 2145 Planarity : 0.004 0.044 2172 Dihedral : 6.743 88.317 1873 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.43 % Favored : 94.27 % Rotamer: Outliers : 2.23 % Allowed : 19.60 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 aren not related in a simple way. whole: 0.45 (0.21), residues: 1676 helix: 1.71 (0.19), residues: 789 sheet: -0.05 (0.57), residues: 97 loop : -1.16 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 13 TYR 0.014 0.001 TYR A 56 PHE 0.009 0.001 PHE A 21 TRP 0.011 0.001 TRP D 97 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00218 (12970) covalent geometry : angle 0.54467 (17701) hydrogen bonds : bond 0.03346 ( 606) hydrogen bonds : angle 4.05084 ( 1773) metal coordination : bond 0.00678 ( 43) metal coordination : angle 11.97015 ( 123) Misc. bond : bond 0.00077 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: B 92 MET cc_start: -0.0185 (OUTLIER) cc_final: -0.1723 (ppp) REVERT: B 129 MET cc_start: 0.7662 (tpt) cc_final: 0.6776 (tpt) REVERT: B 230 ASP cc_start: 0.8883 (t0) cc_final: 0.8494 (t0) REVERT: B 245 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8050 (mttp) REVERT: B 309 MET cc_start: 0.2126 (pmm) cc_final: 0.1712 (pmm) REVERT: C 122 MET cc_start: 0.8195 (mmm) cc_final: 0.7240 (mmm) REVERT: C 201 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7534 (mmmt) REVERT: C 226 ARG cc_start: 0.7643 (mtm110) cc_final: 0.6819 (ttp80) REVERT: C 288 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6930 (ttt90) REVERT: C 304 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 343 ASP cc_start: 0.8419 (t0) cc_final: 0.7891 (t0) REVERT: D 66 LYS cc_start: 0.7995 (tppt) cc_final: 0.7070 (ttpt) REVERT: D 129 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6004 (tpp-160) REVERT: D 174 ASP cc_start: 0.7783 (t0) cc_final: 0.6947 (t0) REVERT: D 239 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7133 (t) REVERT: E 4 MET cc_start: 0.5277 (mmt) cc_final: 0.5000 (mmt) REVERT: G 197 MET cc_start: 0.6723 (mtm) cc_final: 0.6501 (ptp) outliers start: 30 outliers final: 22 residues processed: 186 average time/residue: 0.1321 time to fit residues: 34.7872 Evaluate side-chains 179 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 0.0470 chunk 64 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN G 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.193409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138390 restraints weight = 13750.284| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.06 r_work: 0.3302 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13018 Z= 0.131 Angle : 1.170 60.819 17824 Z= 0.303 Chirality : 0.044 0.317 2145 Planarity : 0.004 0.044 2172 Dihedral : 6.739 89.597 1873 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.50 % Favored : 93.20 % Rotamer: Outliers : 2.15 % Allowed : 19.90 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 aren not related in a simple way. whole: 0.50 (0.21), residues: 1676 helix: 1.74 (0.19), residues: 789 sheet: -0.02 (0.58), residues: 97 loop : -1.13 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 13 TYR 0.017 0.001 TYR D 215 PHE 0.015 0.001 PHE A 21 TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00311 (12970) covalent geometry : angle 0.56945 (17701) hydrogen bonds : bond 0.03868 ( 606) hydrogen bonds : angle 4.08850 ( 1773) metal coordination : bond 0.00924 ( 43) metal coordination : angle 12.31048 ( 123) Misc. bond : bond 0.00114 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.39 seconds wall clock time: 53 minutes 18.33 seconds (3198.33 seconds total)