Starting phenix.real_space_refine on Wed Jul 30 17:46:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eri_19915/07_2025/9eri_19915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eri_19915/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eri_19915/07_2025/9eri_19915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eri_19915/07_2025/9eri_19915.map" model { file = "/net/cci-nas-00/data/ceres_data/9eri_19915/07_2025/9eri_19915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eri_19915/07_2025/9eri_19915.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.97, per 1000 atoms: 0.63 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.30 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: 3.49 Time building geometry restraints manager: 3.84 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- 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 : 4.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP D 97 HIS 0.003 0.001 HIS D 18 PHE 0.010 0.001 PHE B 30 TYR 0.018 0.001 TYR D 40 ARG 0.011 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.14901 ( 606) hydrogen bonds : angle 6.04391 ( 1773) metal coordination : bond 0.16197 ( 43) metal coordination : angle 13.39230 ( 123) covalent geometry : bond 0.00584 (12970) covalent geometry : angle 1.03787 (17701) 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 : 1.161 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: 0.2688 time to fit residues: 62.9131 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 : 1.279 ------------------------------------------------------------------------------- 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 140 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.196783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141452 restraints weight = 13687.937| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.76 r_work: 0.3364 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13018 Z= 0.122 Angle : 1.088 65.976 17824 Z= 0.300 Chirality : 0.042 0.223 2145 Planarity : 0.004 0.046 2172 Dihedral : 8.004 87.023 1898 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.61 % Favored : 93.85 % Rotamer: Outliers : 3.12 % Allowed : 16.48 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1676 helix: 1.24 (0.19), residues: 796 sheet: -0.18 (0.53), residues: 107 loop : -1.36 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS D 13 PHE 0.008 0.001 PHE B 30 TYR 0.016 0.001 TYR D 40 ARG 0.005 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 606) hydrogen bonds : angle 4.52588 ( 1773) metal coordination : bond 0.00660 ( 43) metal coordination : angle 11.28663 ( 123) covalent geometry : bond 0.00271 (12970) covalent geometry : angle 0.55310 (17701) Misc. bond : bond 0.00112 ( 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 204 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7254 (m-80) cc_final: 0.6673 (m-80) REVERT: B 155 ASP cc_start: 0.8349 (t70) cc_final: 0.7805 (t70) REVERT: B 245 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7955 (mtmm) REVERT: C 116 TYR cc_start: 0.7983 (m-80) cc_final: 0.7395 (m-80) REVERT: C 122 MET cc_start: 0.7901 (mmm) cc_final: 0.7075 (tmm) REVERT: C 343 ASP cc_start: 0.7916 (t0) cc_final: 0.7482 (t0) REVERT: C 347 MET cc_start: 0.8348 (mmt) cc_final: 0.8061 (mmm) REVERT: D 66 LYS cc_start: 0.7567 (tppt) cc_final: 0.6686 (ttmt) REVERT: D 129 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.5298 (tpp-160) REVERT: D 174 ASP cc_start: 0.7609 (t0) cc_final: 0.7100 (t0) REVERT: E 4 MET cc_start: 0.4980 (mmt) cc_final: 0.4696 (mmt) outliers start: 42 outliers final: 19 residues processed: 196 average time/residue: 0.2419 time to fit residues: 68.3383 Evaluate side-chains 169 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 1 MET 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 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 207 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 193 THR 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 60 optimal weight: 0.2980 chunk 152 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.196620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141234 restraints weight = 13765.288| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.96 r_work: 0.3342 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13018 Z= 0.115 Angle : 1.025 63.523 17824 Z= 0.291 Chirality : 0.042 0.202 2145 Planarity : 0.004 0.043 2172 Dihedral : 7.527 88.184 1879 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.49 % Favored : 94.03 % Rotamer: Outliers : 2.90 % Allowed : 17.22 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1676 helix: 1.45 (0.19), residues: 805 sheet: -0.08 (0.53), residues: 107 loop : -1.31 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS D 13 PHE 0.007 0.001 PHE B 30 TYR 0.014 0.001 TYR D 263 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 606) hydrogen bonds : angle 4.25360 ( 1773) metal coordination : bond 0.00592 ( 43) metal coordination : angle 10.48912 ( 123) covalent geometry : bond 0.00260 (12970) covalent geometry : angle 0.54189 (17701) Misc. bond : bond 0.00092 ( 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 198 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7531 (m-80) cc_final: 0.6915 (m-80) REVERT: B 245 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: B 309 MET cc_start: 0.1533 (ppp) cc_final: 0.1316 (pmm) REVERT: C 116 TYR cc_start: 0.8000 (m-80) cc_final: 0.7451 (m-80) REVERT: C 122 MET cc_start: 0.7991 (mmm) cc_final: 0.7168 (tmm) REVERT: C 201 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7345 (mmmt) REVERT: C 343 ASP cc_start: 0.8021 (t0) cc_final: 0.7596 (t0) REVERT: D 66 LYS cc_start: 0.7693 (tppt) cc_final: 0.6816 (ttpt) REVERT: D 129 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6205 (tpp-160) REVERT: D 174 ASP cc_start: 0.7630 (t0) cc_final: 0.7081 (t0) REVERT: E 1 MET cc_start: 0.4984 (pmm) cc_final: 0.4568 (tmm) REVERT: E 4 MET cc_start: 0.4835 (mmt) cc_final: 0.4491 (tpp) REVERT: E 90 VAL cc_start: 0.6984 (t) cc_final: 0.6549 (m) REVERT: G 34 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6404 (mt) outliers start: 39 outliers final: 20 residues processed: 195 average time/residue: 0.2408 time to fit residues: 67.6880 Evaluate side-chains 176 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 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 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 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 34 LEU 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 90 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.196190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140668 restraints weight = 13645.574| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.92 r_work: 0.3338 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13018 Z= 0.118 Angle : 1.184 61.252 17824 Z= 0.295 Chirality : 0.043 0.266 2145 Planarity : 0.004 0.044 2172 Dihedral : 7.373 87.949 1877 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.85 % Favored : 93.68 % Rotamer: Outliers : 3.41 % Allowed : 16.70 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1676 helix: 1.50 (0.19), residues: 807 sheet: -0.13 (0.53), residues: 108 loop : -1.31 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS D 13 PHE 0.008 0.001 PHE D 131 TYR 0.014 0.001 TYR D 215 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 606) hydrogen bonds : angle 4.18785 ( 1773) metal coordination : bond 0.00704 ( 43) metal coordination : angle 12.69465 ( 123) covalent geometry : bond 0.00272 (12970) covalent geometry : angle 0.53995 (17701) Misc. bond : bond 0.00090 ( 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 208 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.5658 (m-80) REVERT: A 127 TYR cc_start: 0.7648 (m-80) cc_final: 0.7083 (m-80) REVERT: B 92 MET cc_start: 0.0244 (pmm) cc_final: -0.1142 (ppp) REVERT: B 155 ASP cc_start: 0.8380 (t70) cc_final: 0.7890 (t70) REVERT: B 245 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8083 (mttp) REVERT: C 116 TYR cc_start: 0.8051 (m-80) cc_final: 0.7469 (m-80) REVERT: C 122 MET cc_start: 0.8000 (mmm) cc_final: 0.7181 (mmm) REVERT: C 201 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7350 (mmmt) REVERT: C 343 ASP cc_start: 0.8049 (t0) cc_final: 0.7637 (t0) REVERT: D 66 LYS cc_start: 0.7678 (tppt) cc_final: 0.6763 (ttmt) REVERT: D 129 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.5463 (tpp-160) REVERT: D 174 ASP cc_start: 0.7720 (t0) cc_final: 0.7043 (t0) REVERT: E 1 MET cc_start: 0.5203 (pmm) cc_final: 0.4784 (tmm) REVERT: E 4 MET cc_start: 0.4918 (mmt) cc_final: 0.4598 (tpp) REVERT: E 90 VAL cc_start: 0.7040 (t) cc_final: 0.6644 (m) REVERT: G 34 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6369 (mt) outliers start: 46 outliers final: 29 residues processed: 199 average time/residue: 0.2555 time to fit residues: 73.1937 Evaluate side-chains 185 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 181 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 245 LYS 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 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 192 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 34 LEU 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 76 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 0.0010 chunk 127 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.195613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140110 restraints weight = 13411.851| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.77 r_work: 0.3375 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13018 Z= 0.100 Angle : 1.146 65.702 17824 Z= 0.283 Chirality : 0.042 0.215 2145 Planarity : 0.004 0.043 2172 Dihedral : 7.086 86.599 1874 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.37 % Favored : 94.15 % Rotamer: Outliers : 3.12 % Allowed : 17.52 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1676 helix: 1.69 (0.19), residues: 805 sheet: -0.04 (0.54), residues: 107 loop : -1.27 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.002 0.000 HIS D 13 PHE 0.005 0.001 PHE A 27 TYR 0.011 0.001 TYR D 215 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 606) hydrogen bonds : angle 4.03303 ( 1773) metal coordination : bond 0.00735 ( 43) metal coordination : angle 12.31943 ( 123) covalent geometry : bond 0.00217 (12970) covalent geometry : angle 0.51708 (17701) Misc. bond : bond 0.00076 ( 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 200 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: B 92 MET cc_start: 0.0355 (OUTLIER) cc_final: -0.1393 (ppp) REVERT: B 245 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8204 (mttp) REVERT: C 116 TYR cc_start: 0.8040 (m-80) cc_final: 0.7439 (m-80) REVERT: C 122 MET cc_start: 0.8001 (mmm) cc_final: 0.7179 (mmm) REVERT: C 343 ASP cc_start: 0.8054 (t0) cc_final: 0.7633 (t0) REVERT: C 347 MET cc_start: 0.8262 (mmm) cc_final: 0.7849 (mmm) REVERT: D 66 LYS cc_start: 0.7881 (tppt) cc_final: 0.6971 (ttmt) REVERT: D 129 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6103 (tpp-160) REVERT: D 174 ASP cc_start: 0.7880 (t0) cc_final: 0.7131 (t0) REVERT: E 1 MET cc_start: 0.5103 (pmm) cc_final: 0.4850 (tmm) REVERT: E 4 MET cc_start: 0.4899 (mmt) cc_final: 0.4578 (tpp) REVERT: E 90 VAL cc_start: 0.7016 (t) cc_final: 0.6670 (m) REVERT: G 34 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6363 (mt) outliers start: 42 outliers final: 26 residues processed: 192 average time/residue: 0.2606 time to fit residues: 71.4463 Evaluate side-chains 179 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 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 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 156 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 116 GLU 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 127 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.193148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138181 restraints weight = 13614.637| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.91 r_work: 0.3331 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13018 Z= 0.119 Angle : 1.177 65.256 17824 Z= 0.291 Chirality : 0.043 0.228 2145 Planarity : 0.004 0.043 2172 Dihedral : 6.943 88.276 1873 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.67 % Favored : 93.85 % Rotamer: Outliers : 3.41 % Allowed : 17.67 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1676 helix: 1.74 (0.19), residues: 798 sheet: 0.00 (0.54), residues: 107 loop : -1.21 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 45 HIS 0.002 0.001 HIS D 13 PHE 0.009 0.001 PHE D 131 TYR 0.015 0.001 TYR D 263 ARG 0.004 0.000 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 606) hydrogen bonds : angle 4.06250 ( 1773) metal coordination : bond 0.00806 ( 43) metal coordination : angle 12.64853 ( 123) covalent geometry : bond 0.00278 (12970) covalent geometry : angle 0.53286 (17701) Misc. bond : bond 0.00084 ( 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: 46 poor density : 170 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: B 92 MET cc_start: 0.0154 (OUTLIER) cc_final: -0.1548 (ppp) REVERT: B 230 ASP cc_start: 0.8546 (t0) cc_final: 0.8246 (t0) REVERT: B 245 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8215 (mttp) REVERT: C 116 TYR cc_start: 0.8087 (m-80) cc_final: 0.7506 (m-80) REVERT: C 122 MET cc_start: 0.8104 (mmm) cc_final: 0.7431 (mmm) REVERT: C 343 ASP cc_start: 0.8168 (t0) cc_final: 0.7542 (t0) REVERT: C 347 MET cc_start: 0.8319 (mmm) cc_final: 0.7864 (mmm) REVERT: D 66 LYS cc_start: 0.7943 (tppt) cc_final: 0.7013 (ttpt) REVERT: D 129 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6120 (tpp-160) REVERT: D 174 ASP cc_start: 0.7948 (t0) cc_final: 0.7119 (t0) REVERT: E 1 MET cc_start: 0.5112 (pmm) cc_final: 0.4911 (tmm) REVERT: E 4 MET cc_start: 0.4989 (mmt) cc_final: 0.4717 (mmt) REVERT: E 90 VAL cc_start: 0.7012 (t) cc_final: 0.6704 (m) outliers start: 46 outliers final: 34 residues processed: 203 average time/residue: 0.2444 time to fit residues: 71.5162 Evaluate side-chains 197 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 A residue 181 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 186 ILE 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 34 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 156 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 G 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.190506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135449 restraints weight = 13776.870| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.94 r_work: 0.3270 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1702 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= 0.187 Angle : 1.243 63.584 17824 Z= 0.326 Chirality : 0.046 0.234 2145 Planarity : 0.004 0.043 2172 Dihedral : 7.048 88.018 1872 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.50 % Favored : 93.08 % Rotamer: Outliers : 3.93 % Allowed : 17.37 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1676 helix: 1.59 (0.19), residues: 789 sheet: -0.11 (0.53), residues: 107 loop : -1.30 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 45 HIS 0.003 0.001 HIS C 13 PHE 0.014 0.001 PHE D 131 TYR 0.021 0.002 TYR D 263 ARG 0.003 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 606) hydrogen bonds : angle 4.26267 ( 1773) metal coordination : bond 0.01288 ( 43) metal coordination : angle 13.10327 ( 123) covalent geometry : bond 0.00467 (12970) covalent geometry : angle 0.60319 (17701) Misc. bond : bond 0.00135 ( 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 215 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6728 (tmm) cc_final: 0.6383 (tmm) REVERT: B 92 MET cc_start: 0.0139 (OUTLIER) cc_final: -0.1620 (ppp) REVERT: B 230 ASP cc_start: 0.8640 (t0) cc_final: 0.8343 (t0) REVERT: B 245 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8132 (mttp) REVERT: C 107 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: C 116 TYR cc_start: 0.8126 (m-80) cc_final: 0.7555 (m-80) REVERT: C 122 MET cc_start: 0.8239 (mmm) cc_final: 0.7432 (mmm) REVERT: C 334 MET cc_start: 0.8971 (mmm) cc_final: 0.8675 (mmm) REVERT: C 343 ASP cc_start: 0.8269 (t0) cc_final: 0.7789 (t0) REVERT: D 66 LYS cc_start: 0.7993 (tppt) cc_final: 0.7068 (ttpt) REVERT: D 129 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6316 (tpp-160) REVERT: D 174 ASP cc_start: 0.7858 (t0) cc_final: 0.7014 (t0) REVERT: E 4 MET cc_start: 0.5120 (mmt) cc_final: 0.4841 (mmt) REVERT: E 90 VAL cc_start: 0.6924 (t) cc_final: 0.6559 (m) REVERT: G 34 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6404 (mt) outliers start: 53 outliers final: 38 residues processed: 198 average time/residue: 0.2589 time to fit residues: 73.2593 Evaluate side-chains 197 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 186 ILE 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 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 141 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 207 ILE 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 34 LEU 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 139 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.194586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139490 restraints weight = 13844.987| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.15 r_work: 0.3307 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13018 Z= 0.114 Angle : 1.170 62.060 17824 Z= 0.292 Chirality : 0.043 0.231 2145 Planarity : 0.004 0.043 2172 Dihedral : 6.813 89.597 1872 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.97 % Rotamer: Outliers : 3.49 % Allowed : 17.82 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1676 helix: 1.74 (0.19), residues: 794 sheet: 0.00 (0.56), residues: 97 loop : -1.18 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS D 13 PHE 0.014 0.001 PHE A 21 TYR 0.014 0.001 TYR A 56 ARG 0.008 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 606) hydrogen bonds : angle 4.08960 ( 1773) metal coordination : bond 0.00779 ( 43) metal coordination : angle 12.51923 ( 123) covalent geometry : bond 0.00261 (12970) covalent geometry : angle 0.53696 (17701) Misc. bond : bond 0.00081 ( 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 219 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: -0.0210 (OUTLIER) cc_final: -0.1784 (ppp) REVERT: B 230 ASP cc_start: 0.8782 (t0) cc_final: 0.8357 (t0) REVERT: B 245 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: C 52 LYS cc_start: 0.8092 (pttt) cc_final: 0.7880 (ptpp) REVERT: C 107 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: C 116 TYR cc_start: 0.8157 (m-80) cc_final: 0.7571 (m-80) REVERT: C 122 MET cc_start: 0.8201 (mmm) cc_final: 0.7268 (mmm) REVERT: C 334 MET cc_start: 0.8957 (mmm) cc_final: 0.8630 (mmm) REVERT: C 343 ASP cc_start: 0.8393 (t0) cc_final: 0.7829 (t0) REVERT: D 66 LYS cc_start: 0.8022 (tppt) cc_final: 0.7106 (ttpt) REVERT: D 129 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6232 (tpp-160) REVERT: D 174 ASP cc_start: 0.7842 (t0) cc_final: 0.6996 (t0) REVERT: E 4 MET cc_start: 0.5075 (mmt) cc_final: 0.4816 (mmt) REVERT: E 90 VAL cc_start: 0.6792 (t) cc_final: 0.6457 (m) REVERT: G 34 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6397 (mt) outliers start: 47 outliers final: 31 residues processed: 207 average time/residue: 0.2591 time to fit residues: 77.0996 Evaluate side-chains 197 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 ASN Chi-restraints excluded: chain A residue 132 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 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 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 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain G residue 34 LEU 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 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 HIS G 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141188 restraints weight = 13669.589| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.08 r_work: 0.3336 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13018 Z= 0.102 Angle : 1.139 61.675 17824 Z= 0.284 Chirality : 0.042 0.272 2145 Planarity : 0.004 0.043 2172 Dihedral : 6.666 89.231 1872 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.09 % Favored : 93.62 % Rotamer: Outliers : 2.67 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1676 helix: 1.90 (0.19), residues: 788 sheet: 0.09 (0.58), residues: 97 loop : -1.10 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 97 HIS 0.002 0.000 HIS D 13 PHE 0.012 0.001 PHE A 21 TYR 0.012 0.001 TYR A 56 ARG 0.008 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 606) hydrogen bonds : angle 4.00901 ( 1773) metal coordination : bond 0.00683 ( 43) metal coordination : angle 12.16634 ( 123) covalent geometry : bond 0.00221 (12970) covalent geometry : angle 0.52771 (17701) Misc. bond : bond 0.00071 ( 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 193 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: -0.0147 (OUTLIER) cc_final: -0.1695 (ppp) REVERT: B 129 MET cc_start: 0.7706 (tpt) cc_final: 0.6909 (tpt) REVERT: B 230 ASP cc_start: 0.8828 (t0) cc_final: 0.8409 (t0) REVERT: B 245 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: C 107 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: C 116 TYR cc_start: 0.8178 (m-80) cc_final: 0.7561 (m-80) REVERT: C 122 MET cc_start: 0.8111 (mmm) cc_final: 0.7170 (mmm) REVERT: C 343 ASP cc_start: 0.8380 (t0) cc_final: 0.7831 (t0) REVERT: D 66 LYS cc_start: 0.8007 (tppt) cc_final: 0.7090 (ttpt) REVERT: D 129 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6034 (tpp-160) REVERT: D 174 ASP cc_start: 0.7807 (t0) cc_final: 0.6939 (t0) REVERT: E 4 MET cc_start: 0.5109 (mmt) cc_final: 0.4862 (mmt) outliers start: 36 outliers final: 29 residues processed: 185 average time/residue: 0.2772 time to fit residues: 72.8056 Evaluate side-chains 185 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 77 ILE 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 132 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 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 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 86 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140362 restraints weight = 13685.500| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.00 r_work: 0.3338 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13018 Z= 0.108 Angle : 1.136 62.952 17824 Z= 0.289 Chirality : 0.043 0.262 2145 Planarity : 0.004 0.043 2172 Dihedral : 6.569 89.666 1872 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.85 % Favored : 93.85 % Rotamer: Outliers : 2.52 % Allowed : 19.67 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1676 helix: 1.88 (0.19), residues: 789 sheet: 0.13 (0.58), residues: 97 loop : -1.11 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.000 HIS D 13 PHE 0.012 0.001 PHE A 21 TYR 0.013 0.001 TYR A 56 ARG 0.009 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 606) hydrogen bonds : angle 4.02647 ( 1773) metal coordination : bond 0.00702 ( 43) metal coordination : angle 12.06394 ( 123) covalent geometry : bond 0.00243 (12970) covalent geometry : angle 0.53761 (17701) Misc. bond : bond 0.00074 ( 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 187 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: -0.0145 (OUTLIER) cc_final: -0.1690 (ppp) REVERT: B 129 MET cc_start: 0.7696 (tpt) cc_final: 0.6801 (tpt) REVERT: B 230 ASP cc_start: 0.8841 (t0) cc_final: 0.8439 (t0) REVERT: B 245 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8099 (mttp) REVERT: C 107 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: C 122 MET cc_start: 0.8124 (mmm) cc_final: 0.7185 (mmm) REVERT: C 201 LYS cc_start: 0.8251 (mttp) cc_final: 0.7496 (mmmt) REVERT: C 226 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7290 (mtm110) REVERT: C 343 ASP cc_start: 0.8356 (t0) cc_final: 0.7894 (t0) REVERT: D 66 LYS cc_start: 0.8040 (tppt) cc_final: 0.7102 (ttpt) REVERT: D 129 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6225 (tpp-160) REVERT: D 174 ASP cc_start: 0.7950 (t0) cc_final: 0.7060 (t0) REVERT: E 4 MET cc_start: 0.5172 (mmt) cc_final: 0.4901 (mmt) outliers start: 34 outliers final: 30 residues processed: 180 average time/residue: 0.2774 time to fit residues: 71.2667 Evaluate side-chains 185 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 77 ILE 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 132 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 229 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 THR 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 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 85 LEU Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 128 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.194851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139335 restraints weight = 13724.364| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.98 r_work: 0.3324 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13018 Z= 0.117 Angle : 1.137 61.874 17824 Z= 0.292 Chirality : 0.043 0.265 2145 Planarity : 0.004 0.044 2172 Dihedral : 6.571 89.530 1871 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer: Outliers : 2.60 % Allowed : 19.75 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1676 helix: 1.85 (0.19), residues: 789 sheet: 0.04 (0.58), residues: 97 loop : -1.11 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.002 0.001 HIS D 13 PHE 0.014 0.001 PHE A 21 TYR 0.015 0.001 TYR D 263 ARG 0.009 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 606) hydrogen bonds : angle 4.04367 ( 1773) metal coordination : bond 0.00801 ( 43) metal coordination : angle 12.02511 ( 123) covalent geometry : bond 0.00270 (12970) covalent geometry : angle 0.54460 (17701) Misc. bond : bond 0.00079 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6506.88 seconds wall clock time: 113 minutes 30.94 seconds (6810.94 seconds total)