Starting phenix.real_space_refine on Wed Jun 11 06:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.map" model { file = "/net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erl_19920/06_2025/9erl_19920.cif" } resolution = 3.0 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= -0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Fe 42 7.16 5 P 3 5.49 5 S 158 5.16 5 Na 3 4.78 5 C 8074 2.51 5 N 2063 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12663 Number of models: 1 Model: "" Number of chains: 12 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: {'PTRANS': 29, '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: {'PTRANS': 5, 'TRANS': 201} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NA': 2, 'FES': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 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 49.065 61.737 58.296 1.00 0.00 S ATOM 10283 SG CYS E 108 47.405 63.927 56.132 1.00 10.16 S ATOM 857 SG CYS A 113 46.585 59.492 52.416 1.00 9.03 S ATOM 9687 SG CYS E 25 49.146 57.981 54.837 1.00 4.98 S ATOM 2824 SG CYS B 200 58.448 82.783 112.504 1.00 0.00 S ATOM 2373 SG CYS B 138 57.848 76.410 113.523 1.00 0.00 S ATOM 2927 SG CYS B 213 63.487 79.003 113.603 1.00 6.70 S ATOM 2142 SG CYS B 106 60.113 78.731 107.856 1.00 0.00 S ATOM 2406 SG CYS B 142 59.526 74.644 103.119 1.00 0.00 S ATOM 2688 SG CYS B 182 53.192 75.575 101.549 1.00 0.00 S ATOM 2288 SG CYS B 125 56.133 69.821 100.889 1.00 0.00 S ATOM 2447 SG CYS B 148 57.201 74.806 96.951 1.00 0.00 S ATOM 1840 SG CYS B 58 44.015 80.798 77.033 1.00 93.31 S ATOM 1797 SG CYS B 50 47.873 80.588 82.611 1.00 68.59 S ATOM 1811 SG CYS B 53 43.086 78.656 82.750 1.00 82.39 S ATOM 1945 SG CYS B 75 44.316 85.473 81.469 1.00 82.50 S ATOM 2474 SG CYS B 152 56.560 77.391 88.649 1.00 5.26 S ATOM 2642 SG CYS B 175 51.142 80.965 88.368 1.00 17.12 S ATOM 2623 SG CYS B 172 56.099 84.077 90.125 1.00 20.37 S ATOM 2661 SG CYS B 178 53.670 79.575 93.867 1.00 0.00 S ATOM 3219 SG CYS B 252 59.751 97.521 110.245 1.00 30.07 S ATOM 3013 SG CYS B 227 54.810 101.442 110.861 1.00 34.74 S ATOM 3166 SG CYS B 246 56.575 99.052 104.874 1.00 32.80 S ATOM 2971 SG CYS B 220 59.278 91.626 120.522 1.00 19.58 S ATOM 2952 SG CYS B 217 56.855 87.582 115.861 1.00 7.90 S ATOM 3249 SG CYS B 256 62.417 90.925 115.168 1.00 20.06 S ATOM 2986 SG CYS B 223 56.801 94.088 115.440 1.00 37.69 S ATOM 3488 SG CYS B 289 59.652 117.603 107.179 1.00103.00 S ATOM 3668 SG CYS B 313 58.794 110.897 105.639 1.00 58.31 S ATOM 3650 SG CYS B 310 64.114 112.910 107.349 1.00 76.61 S ATOM 3686 SG CYS B 316 60.871 115.014 101.739 1.00 79.68 S ATOM 3720 SG CYS B 320 57.950 120.195 98.390 1.00 94.03 S ATOM 3423 SG CYS B 279 61.244 125.388 97.094 1.00 93.17 S ATOM 3442 SG CYS B 282 58.779 126.429 97.916 1.00 98.50 S ATOM 3460 SG CYS B 285 61.612 122.739 102.628 1.00 92.67 S ATOM 6565 SG CYS C 372 50.269 41.807 93.282 1.00 0.00 S ATOM 6915 SG CYS C 418 52.058 46.512 96.777 1.00 0.00 S ATOM 6584 SG CYS C 375 46.089 45.944 94.333 1.00 0.00 S ATOM 6541 SG CYS C 369 51.333 47.730 90.516 1.00 0.00 S ATOM 6867 SG CYS C 411 40.367 47.761 104.682 1.00 0.00 S ATOM 6844 SG CYS C 408 39.787 53.286 101.432 1.00 0.00 S ATOM 6608 SG CYS C 379 38.771 47.410 98.538 1.00 0.00 S ATOM 6883 SG CYS C 414 44.714 49.382 100.582 1.00 0.00 S Time building chain proxies: 8.93, per 1000 atoms: 0.71 Number of scatterers: 12663 At special positions: 0 Unit cell: (88.16, 142.12, 158.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 42 26.01 S 158 16.00 P 3 15.00 Na 3 11.00 O 2320 8.00 N 2063 7.00 C 8074 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 203 " pdb="FE1 FES A 203 " - pdb=" SG CYS E 108 " pdb="FE1 FES A 203 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 203 " - pdb=" SG CYS E 25 " pdb="FE2 FES A 203 " - pdb=" SG CYS A 113 " 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="FE1 SF4 B 401 " - pdb=" SG CYS B 200 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 213 " pdb=" SF4 B 402 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 182 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 148 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 125 " pdb=" SF4 B 403 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 50 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 75 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 58 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 53 " pdb=" SF4 B 404 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 175 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 172 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 178 " pdb=" SF4 B 405 " 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="FE1 SF4 B 406 " - pdb=" SG CYS B 220 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 223 " pdb="FE3 SF4 B 406 " - pdb=" SG CYS B 256 " pdb="FE2 SF4 B 406 " - pdb=" SG CYS B 217 " pdb=" SF4 B 407 " pdb="FE2 SF4 B 407 " - pdb=" SG CYS B 313 " pdb="FE4 SF4 B 407 " - pdb=" SG CYS B 316 " pdb="FE1 SF4 B 407 " - pdb=" SG CYS B 289 " pdb="FE3 SF4 B 407 " - pdb=" SG CYS B 310 " pdb=" SF4 B 408 " pdb="FE1 SF4 B 408 " - pdb=" SG CYS B 320 " pdb="FE4 SF4 B 408 " - pdb=" SG CYS B 285 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 282 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 279 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 372 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 418 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 375 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 369 " pdb=" SF4 C 502 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 411 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 408 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 379 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 414 " 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: 64 helices and 12 sheets defined 48.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.522A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.698A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.381A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 106 through 110 removed outlier: 4.023A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 128 through 158 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.633A pdb=" N ILE A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 31 Proline residue: B 8 - end of helix Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.582A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 221 through 227 removed outlier: 4.087A pdb=" N LYS B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 227' Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.560A pdb=" N ASP B 318 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.460A pdb=" N GLU C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.629A pdb=" N LYS C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.748A pdb=" N GLN C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 239 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 240 " --> pdb=" O PRO C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.602A pdb=" N VAL C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.613A pdb=" N GLY C 377 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.601A pdb=" N ILE C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 423 through 439 Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.515A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 44 through 68 removed outlier: 3.683A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 49 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 4.049A 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 removed outlier: 3.854A pdb=" N VAL D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.401A pdb=" N GLY D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 190 through 205 removed outlier: 4.158A pdb=" N LEU D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.648A pdb=" N LEU D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.562A pdb=" N MET D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 292 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'E' and resid 3 through 10 removed outlier: 4.383A pdb=" N GLY E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 removed outlier: 3.621A pdb=" N THR E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 58 removed outlier: 3.584A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 90 removed outlier: 3.604A pdb=" N ALA E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.542A pdb=" N ILE E 104 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 122 through 154 removed outlier: 3.862A pdb=" N SER E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 151 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 195 removed outlier: 4.237A pdb=" N PHE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.743A pdb=" N LYS G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 8 through 57 removed outlier: 3.926A pdb=" N LYS G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE G 15 " --> pdb=" O TRP G 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 17 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 19 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU G 34 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.996A pdb=" N ALA G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.836A 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 151 through 156 removed outlier: 3.678A pdb=" N GLN G 154 " --> pdb=" O TRP G 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 156 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 104 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.298A 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 232 through 235 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.398A pdb=" N LYS C 4 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY C 202 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR C 230 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 204 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 232 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 206 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 8.345A pdb=" N ILE C 353 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 291 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS C 355 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 293 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N THR C 357 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY C 352 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER C 330 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 354 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 328 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 356 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.668A pdb=" N ALA C 84 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU C 102 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 82 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.416A pdb=" N VAL C 74 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 67 removed outlier: 3.543A pdb=" N GLU G 90 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY G 102 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER G 96 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 165 through 167 572 hydrogen bonds defined for protein. 1665 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: 3.27 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4949 1.42 - 1.64: 7678 1.64 - 1.86: 171 1.86 - 2.07: 0 2.07 - 2.29: 124 Bond restraints: 12922 Sorted by residual: bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C4 FMN G 301 " pdb=" C4A FMN G 301 " ideal model delta sigma weight residual 1.485 1.407 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C4 FMN C 503 " pdb=" C4A FMN C 503 " ideal model delta sigma weight residual 1.485 1.408 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' FMN C 503 " pdb=" P FMN C 503 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.617 0.059 2.00e-02 2.50e+03 8.67e+00 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17225 2.00 - 4.00: 314 4.00 - 5.99: 65 5.99 - 7.99: 20 7.99 - 9.99: 4 Bond angle restraints: 17628 Sorted by residual: angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" CB PRO B 290 " ideal model delta sigma weight residual 103.25 98.15 5.10 1.05e+00 9.07e-01 2.36e+01 angle pdb=" CA PRO B 290 " pdb=" CB PRO B 290 " pdb=" CG PRO B 290 " ideal model delta sigma weight residual 104.50 95.41 9.09 1.90e+00 2.77e-01 2.29e+01 angle pdb=" C GLY A 103 " pdb=" N VAL A 104 " pdb=" CA VAL A 104 " ideal model delta sigma weight residual 121.97 130.40 -8.43 1.80e+00 3.09e-01 2.19e+01 angle pdb=" N GLY E 98 " pdb=" CA GLY E 98 " pdb=" C GLY E 98 " ideal model delta sigma weight residual 112.73 117.45 -4.72 1.20e+00 6.94e-01 1.55e+01 angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" C PRO B 290 " ideal model delta sigma weight residual 112.47 120.44 -7.97 2.06e+00 2.36e-01 1.50e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6646 17.81 - 35.61: 818 35.61 - 53.42: 174 53.42 - 71.22: 33 71.22 - 89.03: 9 Dihedral angle restraints: 7680 sinusoidal: 2904 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 -130.55 -49.45 0 5.00e+00 4.00e-02 9.78e+01 dihedral pdb=" CA LEU B 45 " pdb=" C LEU B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta harmonic sigma weight residual -180.00 -147.38 -32.62 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ARG E 9 " pdb=" C ARG E 9 " pdb=" N GLY E 10 " pdb=" CA GLY E 10 " ideal model delta harmonic sigma weight residual 180.00 149.65 30.35 0 5.00e+00 4.00e-02 3.68e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1911 0.073 - 0.146: 215 0.146 - 0.219: 10 0.219 - 0.292: 0 0.292 - 0.364: 1 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CB VAL A 104 " pdb=" CA VAL A 104 " pdb=" CG1 VAL A 104 " pdb=" CG2 VAL A 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA PRO B 290 " pdb=" N PRO B 290 " pdb=" C PRO B 290 " pdb=" CB PRO B 290 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PRO B 46 " pdb=" N PRO B 46 " pdb=" C PRO B 46 " pdb=" CB PRO B 46 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2134 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 45 " 0.081 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO B 46 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 166 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C THR D 166 " 0.050 2.00e-02 2.50e+03 pdb=" O THR D 166 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 167 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 111 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C THR A 111 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 111 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 112 " -0.016 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3084 2.80 - 3.32: 10945 3.32 - 3.85: 19066 3.85 - 4.37: 21632 4.37 - 4.90: 39328 Nonbonded interactions: 94055 Sorted by model distance: nonbonded pdb=" O THR B 173 " pdb=" OG1 THR B 173 " model vdw 2.271 3.040 nonbonded pdb=" O ILE B 294 " pdb=" NZ LYS B 299 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP C 208 " pdb=" OG1 THR C 234 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 119 " pdb=" O GLU B 122 " model vdw 2.315 3.040 nonbonded pdb=" O PRO D 137 " pdb=" OG1 THR D 141 " model vdw 2.326 3.040 ... (remaining 94050 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: 4.500 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.700 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12967 Z= 0.201 Angle : 1.131 49.915 17751 Z= 0.395 Chirality : 0.045 0.364 2137 Planarity : 0.007 0.123 2169 Dihedral : 16.244 89.029 4630 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.92 % Favored : 92.60 % Rotamer: Outliers : 1.41 % Allowed : 20.12 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 2.47 % 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: -0.77 (0.20), residues: 1676 helix: 0.78 (0.19), residues: 752 sheet: 0.41 (0.51), residues: 104 loop : -1.95 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 191 HIS 0.002 0.001 HIS B 201 PHE 0.013 0.001 PHE D 131 TYR 0.022 0.001 TYR D 263 ARG 0.003 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.16605 ( 568) hydrogen bonds : angle 6.20587 ( 1665) metal coordination : bond 0.00817 ( 43) metal coordination : angle 10.58855 ( 123) covalent geometry : bond 0.00371 (12922) covalent geometry : angle 0.71184 (17628) Misc. bond : bond 0.04496 ( 2) *********************** 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 173 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 171 average time/residue: 1.1375 time to fit residues: 213.0191 Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 290 PRO Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN G 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.068197 restraints weight = 22123.076| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.23 r_work: 0.2680 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.130 Angle : 1.035 46.750 17751 Z= 0.318 Chirality : 0.043 0.253 2137 Planarity : 0.005 0.122 2169 Dihedral : 5.761 54.562 1824 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.32 % Favored : 93.20 % Rotamer: Outliers : 2.82 % Allowed : 20.34 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.68 (0.20), residues: 762 sheet: 0.22 (0.51), residues: 113 loop : -1.84 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 11 HIS 0.001 0.000 HIS C 42 PHE 0.008 0.001 PHE D 131 TYR 0.020 0.001 TYR D 263 ARG 0.007 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 568) hydrogen bonds : angle 4.19322 ( 1665) metal coordination : bond 0.00888 ( 43) metal coordination : angle 10.18512 ( 123) covalent geometry : bond 0.00283 (12922) covalent geometry : angle 0.59645 (17628) Misc. bond : bond 0.00015 ( 2) *********************** 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 165 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 342 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8440 (m) REVERT: D 165 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7983 (mt-10) outliers start: 38 outliers final: 12 residues processed: 150 average time/residue: 1.4082 time to fit residues: 230.7292 Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 6 optimal weight: 0.0670 chunk 145 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 155 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 147 optimal weight: 6.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN G 179 GLN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.069402 restraints weight = 22244.947| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.30 r_work: 0.2741 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 12967 Z= 0.111 Angle : 0.993 43.341 17751 Z= 0.298 Chirality : 0.043 0.333 2137 Planarity : 0.005 0.120 2169 Dihedral : 5.474 56.969 1812 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.03 % Favored : 93.56 % Rotamer: Outliers : 2.38 % Allowed : 21.75 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.28 (0.22), residues: 1676 helix: 1.99 (0.20), residues: 759 sheet: 0.32 (0.51), residues: 112 loop : -1.73 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 97 HIS 0.002 0.000 HIS C 42 PHE 0.013 0.001 PHE G 15 TYR 0.018 0.001 TYR A 99 ARG 0.007 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 568) hydrogen bonds : angle 3.87588 ( 1665) metal coordination : bond 0.00662 ( 43) metal coordination : angle 9.84842 ( 123) covalent geometry : bond 0.00232 (12922) covalent geometry : angle 0.56213 (17628) Misc. bond : bond 0.00035 ( 2) *********************** 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 166 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 342 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8542 (m) REVERT: D 165 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 121 ASN cc_start: 0.7476 (m-40) cc_final: 0.6967 (m-40) REVERT: G 153 ASP cc_start: 0.9011 (p0) cc_final: 0.8738 (p0) outliers start: 32 outliers final: 11 residues processed: 154 average time/residue: 1.3877 time to fit residues: 233.4285 Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.067200 restraints weight = 22057.437| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.25 r_work: 0.2667 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.125 Angle : 0.983 42.441 17751 Z= 0.304 Chirality : 0.044 0.377 2137 Planarity : 0.005 0.120 2169 Dihedral : 5.433 57.142 1812 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.56 % Favored : 93.02 % Rotamer: Outliers : 2.75 % Allowed : 21.31 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.38 (0.22), residues: 1676 helix: 2.09 (0.20), residues: 759 sheet: 0.42 (0.49), residues: 118 loop : -1.72 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.001 0.000 HIS C 42 PHE 0.010 0.001 PHE G 15 TYR 0.020 0.001 TYR D 263 ARG 0.008 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 568) hydrogen bonds : angle 3.83132 ( 1665) metal coordination : bond 0.00732 ( 43) metal coordination : angle 9.57385 ( 123) covalent geometry : bond 0.00281 (12922) covalent geometry : angle 0.57791 (17628) Misc. bond : bond 0.00010 ( 2) *********************** 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 166 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 VAL cc_start: 0.6736 (m) cc_final: 0.6500 (p) REVERT: B 40 LEU cc_start: 0.9054 (mt) cc_final: 0.8807 (tm) REVERT: E 121 ASN cc_start: 0.7588 (m-40) cc_final: 0.7110 (m-40) REVERT: G 82 MET cc_start: 0.6352 (ttp) cc_final: 0.6132 (ttp) REVERT: G 153 ASP cc_start: 0.9040 (p0) cc_final: 0.8765 (p0) REVERT: G 168 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.4959 (ttmm) outliers start: 37 outliers final: 17 residues processed: 150 average time/residue: 1.5056 time to fit residues: 245.2501 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 168 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN G 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061586 restraints weight = 22105.415| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.23 r_work: 0.2556 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12967 Z= 0.207 Angle : 1.047 41.905 17751 Z= 0.345 Chirality : 0.047 0.298 2137 Planarity : 0.005 0.119 2169 Dihedral : 5.742 59.881 1812 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.10 % Favored : 92.48 % Rotamer: Outliers : 2.97 % Allowed : 21.46 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.97 (0.20), residues: 758 sheet: 0.35 (0.48), residues: 118 loop : -1.79 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 97 HIS 0.003 0.001 HIS B 201 PHE 0.014 0.001 PHE D 131 TYR 0.027 0.002 TYR D 263 ARG 0.006 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.07202 ( 568) hydrogen bonds : angle 4.14598 ( 1665) metal coordination : bond 0.01112 ( 43) metal coordination : angle 9.83445 ( 123) covalent geometry : bond 0.00506 (12922) covalent geometry : angle 0.65427 (17628) Misc. bond : bond 0.00048 ( 2) *********************** 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 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9156 (m-80) cc_final: 0.8881 (m-80) REVERT: A 124 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 164 LYS cc_start: 0.8597 (tppt) cc_final: 0.7863 (pmtt) REVERT: B 40 LEU cc_start: 0.9152 (mt) cc_final: 0.8825 (tm) REVERT: D 61 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: D 315 GLU cc_start: 0.2042 (OUTLIER) cc_final: 0.1500 (mp0) REVERT: E 121 ASN cc_start: 0.8016 (m-40) cc_final: 0.7548 (m-40) REVERT: G 82 MET cc_start: 0.6388 (ttp) cc_final: 0.6120 (ttp) REVERT: G 153 ASP cc_start: 0.9108 (p0) cc_final: 0.8830 (p0) REVERT: G 168 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.4756 (tppp) outliers start: 40 outliers final: 21 residues processed: 155 average time/residue: 1.2018 time to fit residues: 204.3152 Evaluate side-chains 149 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 165 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.064763 restraints weight = 22599.568| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.26 r_work: 0.2627 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12967 Z= 0.125 Angle : 0.992 40.066 17751 Z= 0.314 Chirality : 0.044 0.363 2137 Planarity : 0.005 0.118 2169 Dihedral : 5.557 58.041 1811 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.50 % Rotamer: Outliers : 2.30 % Allowed : 23.16 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.45 (0.22), residues: 1676 helix: 2.23 (0.20), residues: 756 sheet: 0.30 (0.51), residues: 112 loop : -1.72 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.002 0.000 HIS C 42 PHE 0.008 0.001 PHE G 15 TYR 0.020 0.001 TYR D 263 ARG 0.010 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 568) hydrogen bonds : angle 3.85686 ( 1665) metal coordination : bond 0.00672 ( 43) metal coordination : angle 9.53479 ( 123) covalent geometry : bond 0.00280 (12922) covalent geometry : angle 0.59684 (17628) Misc. bond : bond 0.00036 ( 2) *********************** 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 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9044 (m-80) cc_final: 0.8781 (m-80) REVERT: A 104 VAL cc_start: 0.6670 (m) cc_final: 0.6466 (p) REVERT: B 40 LEU cc_start: 0.9139 (mt) cc_final: 0.8848 (tm) REVERT: D 61 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: D 315 GLU cc_start: 0.2074 (OUTLIER) cc_final: 0.1525 (mp0) REVERT: E 121 ASN cc_start: 0.8015 (m-40) cc_final: 0.7524 (m-40) REVERT: G 82 MET cc_start: 0.6261 (ttp) cc_final: 0.6006 (ttp) REVERT: G 153 ASP cc_start: 0.9122 (p0) cc_final: 0.8849 (p0) REVERT: G 168 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.4723 (tppp) outliers start: 31 outliers final: 19 residues processed: 147 average time/residue: 1.2081 time to fit residues: 193.7198 Evaluate side-chains 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN G 118 GLN G 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.063881 restraints weight = 22365.461| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.25 r_work: 0.2605 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12967 Z= 0.138 Angle : 0.965 38.838 17751 Z= 0.318 Chirality : 0.044 0.312 2137 Planarity : 0.005 0.117 2169 Dihedral : 5.291 58.085 1811 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.38 % Favored : 93.20 % Rotamer: Outliers : 2.75 % Allowed : 22.87 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.54 (0.22), residues: 1676 helix: 2.35 (0.20), residues: 749 sheet: 0.42 (0.50), residues: 114 loop : -1.70 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 97 HIS 0.002 0.001 HIS C 42 PHE 0.009 0.001 PHE D 131 TYR 0.022 0.001 TYR D 263 ARG 0.009 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 568) hydrogen bonds : angle 3.86001 ( 1665) metal coordination : bond 0.00782 ( 43) metal coordination : angle 8.99670 ( 123) covalent geometry : bond 0.00320 (12922) covalent geometry : angle 0.61132 (17628) Misc. bond : bond 0.00006 ( 2) *********************** 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 162 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9079 (m-80) cc_final: 0.8821 (m-80) REVERT: B 40 LEU cc_start: 0.9113 (mt) cc_final: 0.8827 (tm) REVERT: D 61 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: D 315 GLU cc_start: 0.2065 (OUTLIER) cc_final: 0.1502 (mp0) REVERT: E 121 ASN cc_start: 0.8024 (m-40) cc_final: 0.7533 (m-40) REVERT: G 153 ASP cc_start: 0.9146 (p0) cc_final: 0.8864 (p0) REVERT: G 168 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.4752 (tppp) outliers start: 37 outliers final: 22 residues processed: 152 average time/residue: 1.2764 time to fit residues: 211.4805 Evaluate side-chains 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 133 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.066505 restraints weight = 22442.225| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.25 r_work: 0.2667 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.115 Angle : 0.943 37.556 17751 Z= 0.306 Chirality : 0.043 0.236 2137 Planarity : 0.005 0.116 2169 Dihedral : 5.087 59.336 1811 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.21 % Favored : 93.38 % Rotamer: Outliers : 2.38 % Allowed : 23.46 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.61 (0.22), residues: 1676 helix: 2.37 (0.20), residues: 758 sheet: 0.26 (0.52), residues: 108 loop : -1.62 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 191 HIS 0.002 0.000 HIS C 42 PHE 0.007 0.001 PHE A 27 TYR 0.017 0.001 TYR D 263 ARG 0.009 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 568) hydrogen bonds : angle 3.70988 ( 1665) metal coordination : bond 0.00678 ( 43) metal coordination : angle 8.82231 ( 123) covalent geometry : bond 0.00257 (12922) covalent geometry : angle 0.59346 (17628) Misc. bond : bond 0.00033 ( 2) *********************** 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 158 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9042 (m-80) cc_final: 0.8807 (m-80) REVERT: B 40 LEU cc_start: 0.9094 (mt) cc_final: 0.8821 (tm) REVERT: D 315 GLU cc_start: 0.2146 (OUTLIER) cc_final: 0.1573 (mp0) REVERT: G 153 ASP cc_start: 0.9157 (p0) cc_final: 0.8881 (p0) REVERT: G 168 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.4610 (tppp) outliers start: 32 outliers final: 16 residues processed: 146 average time/residue: 1.2429 time to fit residues: 197.3476 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 79 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 0.0030 chunk 69 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 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 = 0.3526 r_free = 0.3526 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.066327 restraints weight = 22347.236| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.30 r_work: 0.2658 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12967 Z= 0.116 Angle : 0.949 37.121 17751 Z= 0.308 Chirality : 0.042 0.229 2137 Planarity : 0.005 0.115 2169 Dihedral : 4.973 59.596 1811 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.03 % Favored : 93.56 % Rotamer: Outliers : 2.08 % Allowed : 23.90 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.65 (0.22), residues: 1676 helix: 2.41 (0.20), residues: 759 sheet: 0.24 (0.51), residues: 108 loop : -1.60 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 97 HIS 0.002 0.000 HIS C 42 PHE 0.008 0.001 PHE A 27 TYR 0.018 0.001 TYR D 263 ARG 0.011 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 568) hydrogen bonds : angle 3.68229 ( 1665) metal coordination : bond 0.00622 ( 43) metal coordination : angle 8.85124 ( 123) covalent geometry : bond 0.00265 (12922) covalent geometry : angle 0.59994 (17628) Misc. bond : bond 0.00018 ( 2) *********************** 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 152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9078 (m-80) cc_final: 0.8839 (m-80) REVERT: D 315 GLU cc_start: 0.2161 (OUTLIER) cc_final: 0.1580 (mp0) REVERT: E 121 ASN cc_start: 0.7928 (m-40) cc_final: 0.7406 (m-40) REVERT: G 153 ASP cc_start: 0.9154 (p0) cc_final: 0.8897 (p0) REVERT: G 168 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.4556 (tppp) outliers start: 28 outliers final: 20 residues processed: 144 average time/residue: 1.2798 time to fit residues: 200.5836 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN G 118 GLN G 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066553 restraints weight = 22380.522| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.27 r_work: 0.2662 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12967 Z= 0.118 Angle : 0.964 37.516 17751 Z= 0.312 Chirality : 0.042 0.220 2137 Planarity : 0.005 0.114 2169 Dihedral : 4.930 59.844 1811 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.50 % Rotamer: Outliers : 1.63 % Allowed : 24.42 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.70 (0.22), residues: 1676 helix: 2.43 (0.20), residues: 760 sheet: 0.23 (0.51), residues: 108 loop : -1.55 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 97 HIS 0.002 0.000 HIS C 42 PHE 0.008 0.001 PHE A 27 TYR 0.018 0.001 TYR D 263 ARG 0.011 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 568) hydrogen bonds : angle 3.64867 ( 1665) metal coordination : bond 0.00697 ( 43) metal coordination : angle 8.94458 ( 123) covalent geometry : bond 0.00269 (12922) covalent geometry : angle 0.61415 (17628) Misc. bond : bond 0.00022 ( 2) ********************** 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 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9064 (m-80) cc_final: 0.8836 (m-80) REVERT: A 104 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6401 (p) REVERT: D 315 GLU cc_start: 0.2152 (OUTLIER) cc_final: 0.1569 (mp0) REVERT: E 121 ASN cc_start: 0.7910 (m-40) cc_final: 0.7329 (m-40) REVERT: G 153 ASP cc_start: 0.9151 (p0) cc_final: 0.8901 (p0) outliers start: 22 outliers final: 17 residues processed: 140 average time/residue: 1.2698 time to fit residues: 193.3859 Evaluate side-chains 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.064339 restraints weight = 22254.605| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.27 r_work: 0.2616 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12967 Z= 0.139 Angle : 0.989 37.630 17751 Z= 0.325 Chirality : 0.043 0.216 2137 Planarity : 0.005 0.114 2169 Dihedral : 4.984 59.389 1811 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.62 % Favored : 92.96 % Rotamer: Outliers : 2.30 % Allowed : 24.13 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 0.69 (0.22), residues: 1676 helix: 2.42 (0.20), residues: 757 sheet: 0.41 (0.50), residues: 114 loop : -1.58 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 97 HIS 0.002 0.001 HIS B 201 PHE 0.009 0.001 PHE D 131 TYR 0.021 0.001 TYR D 263 ARG 0.011 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 568) hydrogen bonds : angle 3.73998 ( 1665) metal coordination : bond 0.00798 ( 43) metal coordination : angle 9.12112 ( 123) covalent geometry : bond 0.00329 (12922) covalent geometry : angle 0.63534 (17628) Misc. bond : bond 0.00005 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9168.28 seconds wall clock time: 159 minutes 25.31 seconds (9565.31 seconds total)